py4cytoscape Documentation

py4cytoscape DocumentationRelease 0.0.1

The Cytoscape Consortium

Jun 21, 2020

CONTENTS

1 Audience 3

2 Python 5

3 Free Software 7

4 History 9

5 Documentation 11

6 Indices and tables 271

Python Module Index 273

Index 275

i

ii

py4cytoscape Documentation, Release 0.0.1

py4cytoscape is a Python package that communicates with Cytoscape via its REST API, providing access to a set over250 functions that enable control of Cytoscape from within standalone and Notebook Python programming environ-ments. It provides nearly identical functionality to RCy3, an R package in Bioconductor available to R programmers.

py4cytoscape provides:

• functions that can be leveraged from Python code to implement network biology-oriented workflows;

• access to user-written Cytoscape Apps that implement Cytoscape Automation protocols;

• logging and debugging facilities that enable rapid development, maintenance, and auditing of Python-basedworkflow;

• two-way conversion between the igraph and NetworkX graph packages, which enables interoperability withpopular packages available in public repositories (e.g., PyPI); and

• the ability to painlessly work with large data sets generated within Python or available on public repositories(e.g., STRING and NDEx).

With py4cytoscape, you can leverage Cytoscape to:

• load and store networks in standard and nonstandard data formats;

• visualize molecular interaction networks and biological pathways;

• integrate these networks with annotations, gene expression profiles and other state data;

• analyze, profile, and cluster these networks based on integrated data, using new and existing algorithms.

py4cytoscape enables an agile collaboration between powerful Cytoscape, Python libraries, and novel Python code soas to realize auditable, reproducible and sharable workflows.

CONTENTS 1

https://cytoscape.org

https://pubmed.ncbi.nlm.nih.gov/31477170/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880260/

http://apps.cytoscape.org/

https://pubmed.ncbi.nlm.nih.gov/31477170/

https://igraph.org/python/

https://networkx.github.io/documentation/stable/

https://pypi.org/

https://string-db.org/

http://ndexbio.org


2 CONTENTS

CHAPTER

ONE

AUDIENCE

The audience for py4cytoscape includes biologists, mathematicians, physicists, biologists, computer scientists, andsocial scientists. A running sample of research based on Cytoscape can be found on Tumblr. Cytoscape providestutorials, videos, and automation vignettes.

Google Scholar reports that Cytoscape was cited in over 10,000 in academic papers in 2019, most of which executedCytoscape via the traditional mouse and keyboard. py4cytoscape can automate these results as a means of achievingreproducible science.

3

https://cytoscape-publications.tumblr.com/

https://github.com/cytoscape/cytoscape-tutorials/wiki

https://www.youtube.com/channel/UCv6auk9FK4NgXiXiqrDLccw

https://github.com/cytoscape/cytoscape-automation/wiki

https://scholar.google.com/scholar?start=0&q=cytoscape&hl=en&as_sdt=0,5&as_ylo=2019&as_yhi=2019

https://www.nature.com/articles/s41562-016-0021


4 Chapter 1. Audience

CHAPTER

TWO

PYTHON

Python is a powerful programming language that allows simple and flexible representations of networks as well asclear and concise expressions of network algorithms. Python has a vibrant and growing ecosystem of packages thatcan be used in combination with py4cytoscape integrate with traditional workflow engines (e.g., Galaxy and GenePattern) to produce robust end-to-end workflows.

In order to make the most out of py4cytoscape you should know how to write basic programs in Python. Among themany guides to Python, we recommend the Python documentation and Python in a Nutshell.

5

https://galaxyproject.org/

https://www.genepattern.org/

https://www.genepattern.org/

https://docs.python.org/3/

https://www.amazon.com/Python-Nutshell-Second-Alex-Martelli/dp/0596100469


6 Chapter 2. Python

CHAPTER

THREE

FREE SOFTWARE

py4cytoscape is free software; you can redistribute it and/or modify it under the terms of the License. We welcomecontributions. Join us on GitHub.

7

https://github.com/bdemchak/py4cytoscape


8 Chapter 3. Free Software

CHAPTER

FOUR

HISTORY

The original Python libraries for Cytoscape were written by Keiichiro Ono in 2015 as an interface to the then-newCyREST automation interface. Its original name was py2cytoscape. It was further evolved through 2019 by KozoNishida and Jorge Bouças.

In late 2019, py4cytoscape was undertaken by Barry Demchak as a replacement for py2cytoscape. It implemented theAPI defined by RCy3, an R package in Bioconductor developed by a Cytoscape Automation working group consistingof Alex Pico (primary author), Mark Grimes, Julia Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak. RCy3was based on prior work contributed by Paul Shannon, Tanja Muetze, Georgi Kolishkovski and Keiichiro Ono.

We intend to keep the function definitions available through py4cytoscape and RCy3 consistent and synchronizedgoing forward, and to re-integrate unique features found only in py2cytoscape.

9

https://f1000research.com/articles/4-478

https://pypi.org/project/py2cytoscape/


10 Chapter 4. History

CHAPTER

FIVE

DOCUMENTATION

5.1 Install

py4cytoscape requires Python 3.6, 3.7, or 3.8. If you do not already have a Python environment configured onyour computer, please see the instructions for installing the full scientific Python stack.

Note: If you are on Windows and want to install optional packages (e.g., scipy), then you will need to install a Pythondistributions such as Anaconda, Enthought Canopy, Python(x,y), WinPython, or Pyzo. If you use one of these Pythondistribution, please refer to their online documentation.

PyCharm and other integrated development environments often install their own Python distributions.

Below we assume you have the default Python environment already configured on your computer and you intend toinstall py4cytoscape inside of it. If you want to create and work with Python virtual environments, please followinstructions on venv and virtual environments.

First, make sure you have the latest version of pip (the Python package manager) installed. If you do not, refer to thePip documentation and install pip first.

5.1.1 Cytoscape Prerequisite

To exercise py4cytoscape, you must first have downloaded, installed, and executed Cytoscape. If you have notalready done this, please refer to the Launching Cytoscape instructions.

Note: Cytoscape and py4cytoscape must be running on the same workstation or virtual machine.py4cytoscape communicates with Cytoscape via a localhost connection, which precludes py4cytoscape fromaccessing Cytoscape remotely. While this limitation can be overcome by configuring py4cytoscape or supplyingthe Cytoscape URL in py4cytoscape calls, this can become a complex networking problem if firewalls and routersare present on the network.

11

https://scipy.org/install.html

https://www.anaconda.com/download/

https://www.enthought.com/product/canopy

http://python-xy.github.io/

https://winpython.github.io/

http://www.pyzo.org/

https://www.jetbrains.com/pycharm/

https://docs.python.org/3/library/venv.html

http://docs.python-guide.org/en/latest/dev/virtualenvs/

https://pip.pypa.io/en/stable/installing/

http://manual.cytoscape.org/en/stable/Launching_Cytoscape.html#launching-cytoscape


5.1.2 Install the development version (Python Console)

Install the current release of py4cytoscape with pip:

pip install python-igraph requests pandas networkxgit clone git://github.com/bdemchak/py4cytoscapecd py4cytoscapepython setup.py install # or python setup.py install --user

5.1.3 Install the development version (Jupyter Notebook)

Install the current release of py4cytoscape with pip:

!pip install python-igraph requests pandas networkx!pip install git+https://github.com/bdemchak/py4cytoscape!curl localhost:1234

5.1.4 Verify Cytoscape connection

To verify that py4cytoscape is properly installed and able to communicate with Cytoscape, execute the followingin a Python Console or Jupyter Notebook (after starting Cytoscape):

import py4cytoscape as py4dir(py4)py4.cytoscape_ping()py4.cytoscape_version_info()py4.import_network_from_file("tests\data\galfiltered.sif")

This will import py4cytoscape into the Python namespace, print a (long) list of py4cytoscape entrypoints,and then demonstrate a connection to Cytoscape by collecting Cytoscape information and loading a demonstrationnetwork.

5.1.5 Testing

py4cytoscape uses the Python unittest testing package. You can learn more about unittest on its home-page.

To execute tests from an OS command line, set the current directory to the py4cytoscape package directory. Then,establish the execution environment:

cd testsset PYTHONPATH=..

The py4cytoscape test suite consists of a number of sub-suites. Executing one or two of them is relatively quick.To execute a single sub-suite (e.g., test_apps.py):

python -m unittest test_apps.py

To execute more than one sub-suite (e.g., test_apps.py and test_filters.py):

python -m unittest test_apps.py test_filters.py

To execute the entire test suite:

12 Chapter 5. Documentation

https://docs.python.org/3/library/unittest.html

https://docs.python.org/3/library/unittest.html


python -m unittest

To execute a single test (e.g., test_get_app_information) in a single test suite:

python -m unittest test_apps.AppsTests.test_get_app_information

Note: To send test output to a file, redirect stderr and console:

python -m unittest 2>stderr.log 1>cons.log

Some tests require console input, and without console prompts, the tests will appear to stall. To avoid executing suchtests, set the PY4CYTOSCAPE_SKIP_UI_TESTS environment variable described below.

Note: To execute tests with less console debug output, set this environment variable before executing tests:

set PY4CYTOSCAPE_SUMMARY_LOGGER=FALSE

To further configure logging, see the Logging file.

Note: To execute tests without showing test names as tests execute, set this environment variable before executingthe tests:

set PY4CYTOSCAPE_SHOW_TEST_PROGRESS=FALSE

Note: To skip execution of tests that require user input, set this environment variable before executing tests:

set PY4CYTOSCAPE_SKIP_UI_TESTS=TRUE

Note: When executing a large number of tests, we recommend that all three environment variables be set as describedabove.

Note: When executing tests in PyCharm, you can set environment variables using the Run | EditConfigurations... menu item.

5.2 Tutorial

This guide can help you start working with py4cytoscape.

. . . save this space for a simple workflow that Kozo is working on . . .

5.2. Tutorial 13


5.3 Reference

Release 0.0.1

Date Jun 21, 2020

5.3.1 Apps

Functions for inspecting and managing apps for Cytoscape.

Local Apps

disable_app(app[, base_url]) Disable App.enable_app(app[, base_url]) Enable App.get_app_status(app[, base_url]) Retrieve the current status of a Cytoscape app: Installed,

Uninstalled or Disabled.get_app_updates([base_url]) Retrieve list of currently installed Cytoscape apps with

updates available.get_disabled_apps([base_url]) Retrieve list of currently disabled apps in Cytoscape.get_installed_apps([base_url]) Retrieve list of currently installed apps in Cytoscape.get_uninstalled_apps([base_url]) Retrieve list of apps not currently installed in Cytoscape.install_app(app[, base_url]) Installs an app in Cytoscapeuninstall_app(app[, base_url]) Uninstall an app from Cytoscape.update_app(app[, base_url]) Update a Cytoscape app to the latest available version.

py4cytoscape.apps.disable_app

disable_app(app, base_url='http://localhost:1234/v1')Disable App.

Disable an app to effectively remove it from your Cytoscape session without having to uninstall it.

Parameters

• app (str) – Name of app

• base_url (str) – Ignore unless you need to specify a custom domain, port or version toconnect to the CyREST API. Default is http://localhost:1234 and the latest version of theCyREST API supported by this version of py4cytoscape.

Returns {‘appName’: <name of app>}, and is returned whether or not app exists

Return type dict

Raises requests.exceptions.RequestException – if can’t connect to Cytoscape or Cy-toscape returns an error


http://localhost:1234


Examples

>>> disable_app('stringApp'){'appName': 'stringApp'}

py4cytoscape.apps.enable_app

enable_app(app, base_url='http://localhost:1234/v1')Enable App.

Enable a previously installed and disabled app in Cytoscape.

Parameters



Returns {‘appName’: <name of app>}, and is returned whether or not app exists

Return type dict


Examples

>>> enable_app('stringApp'){'appName': 'stringApp'}

py4cytoscape.apps.get_app_status

get_app_status(app, base_url='http://localhost:1234/v1')Retrieve the current status of a Cytoscape app: Installed, Uninstalled or Disabled.

Parameters



Returns {‘appName’: <appname>, ‘status’: <status>} where <status> is Installed, Disabled orUninstalled

Return type dict

Raises

• CyError – if app does not exist

• requests.exceptions.RequestException – if can’t connect to Cytoscape orCytoscape returns an error

5.3. Reference 15




Examples

>>> get_app_status('stringApp'){'appName': 'stringApp', 'status': 'Installed'}

py4cytoscape.apps.get_app_updates

get_app_updates(base_url='http://localhost:1234/v1')Retrieve list of currently installed Cytoscape apps with updates available.

Parameters base_url (str) – Ignore unless you need to specify a custom domain, port or versionto connect to the CyREST API. Default is http://localhost:1234 and the latest version of theCyREST API supported by this version of py4cytoscape.

Returns list of dicts, one for each app {‘appName’: <appname>, ‘version’: <version>, ‘informa-tion’: <information>}

Return type list


Examples

>>> get_app_updates()[{'appName': 'JSON Support', 'version': '3.7.0', 'information': 'null'}, ...]

py4cytoscape.apps.get_disabled_apps

get_disabled_apps(base_url='http://localhost:1234/v1')Retrieve list of currently disabled apps in Cytoscape.


Returns list of dicts, one for each app {‘appName’: <appname>, ‘version’: <version>, ‘descrip-tion’: <description>, ‘status’: <status>} where <status> is always ‘Disabled’

Return type list






Examples

>>> get_disabled_apps()[{'appName': 'stringApp', 'version': '1.4.2', 'description': 'Import and augment→˓Cytoscape networks from STRING', 'status': 'Disabled'}, {...}, ...]

py4cytoscape.apps.get_installed_apps

get_installed_apps(base_url='http://localhost:1234/v1')Retrieve list of currently installed apps in Cytoscape.


Returns list of dicts, one for each app {‘appName’: <appname>, ‘version’: <version>, ‘descrip-tion’: <description>, ‘status’: <status>} where status may be ‘Installed’, ‘Disabled’, ‘Unin-stalled’

Return type list


Examples

>>> get_installed_apps()[{'appName': 'JSON Support', 'version': '3.7.0', 'description': 'null', 'status':→˓'Installed'}, ...]

py4cytoscape.apps.get_uninstalled_apps

get_uninstalled_apps(base_url='http://localhost:1234/v1')Retrieve list of apps not currently installed in Cytoscape.


Returns list of dicts, one for each app {‘appName’: <appname>, ‘version’: <version>, ‘descrip-tion’: <description>, ‘status’: <status>} where status may be ‘Installed’, ‘Disabled’, ‘Unin-stalled’

Return type list


5.3. Reference 17




Examples

>>> get_uninstalled_apps()[{'appName': 'JSON Support', 'version': '3.7.0', 'description': 'null', 'status':→˓'Uninstalled'}, ...]

py4cytoscape.apps.install_app

install_app(app, base_url='http://localhost:1234/v1')Installs an app in Cytoscape

Parameters



Returns {} always empty, whether app exists or not

Return type dict


Examples

>>> install_app('stringApp'){}

py4cytoscape.apps.uninstall_app

uninstall_app(app, base_url='http://localhost:1234/v1')Uninstall an app from Cytoscape.

Parameters



Returns {‘appName’: <name of app>} whether app exists or not

Return type dict






Examples

>>> uninstall_app('stringApp'){'appName': 'stringApp'}

py4cytoscape.apps.update_app

update_app(app, base_url='http://localhost:1234/v1')Update a Cytoscape app to the latest available version.

Parameters



Returns [] whether or not app exists

Return type list


Examples

>>> update_app('stringApp')[]

App Store

get_app_information(app[, base_url]) Retrieve the name, brief description and version of a Cy-toscape app.

get_available_apps([base_url]) Retrieve a list of apps available for installation in Cy-toscape.

open_app_store(app[, base_url]) Opens the Cytoscape App Store in a new tab in yourdefault browser.

py4cytoscape.apps.get_app_information

get_app_information(app, base_url='http://localhost:1234/v1')Retrieve the name, brief description and version of a Cytoscape app.

Parameters



Returns ‘Unused memory freed up.’

5.3. Reference 19




Return type str

Raises

• CyError – if app is unknown


Examples

>>> get_app_information('stringApp'){'app': 'stringApp', 'descriptionName': 'Import and augment Cytoscape networks→˓from STRING', 'version': '1.5.1'}

py4cytoscape.apps.get_available_apps

get_available_apps(base_url='http://localhost:1234/v1')Retrieve a list of apps available for installation in Cytoscape.


Returns list of dicts, one for each app {‘appName’: <appname>, ‘description’: <description>, ‘de-tails’: <details>}

Return type list


Examples

>>> get_available_apps()[{'appName': 'stringApp', 'description': 'Import and augment Cytoscape networks→˓from STRING', 'details': ''}, {...}, ...]

py4cytoscape.apps.open_app_store

open_app_store(app, base_url='http://localhost:1234/v1')Opens the Cytoscape App Store in a new tab in your default browser.

Parameters

• app (str) – Name of app (‘’ for main App Store page)


Returns {} whether page for app exists or not

Return type dict






Examples

>>> open_app_store('stringApp'){}

5.3.2 Collections

Functions for getting information about network COLLECTIONS.

Collections

get_collection_list([base_url]) Get Collection List.get_collection_name([collection_suid,base_url])

Get Collection Name.

get_collection_networks([collection_suid,. . . ])

Get Collection Networks.

get_collection_suid([network, base_url]) Get Collection Suid.

py4cytoscape.collections.get_collection_list

get_collection_list(base_url='http://localhost:1234/v1')Get Collection List.


Returns list of collection names, one for each collection

Return type list


Examples

>>> get_collection_list()[]>>> get_collection_list()['galFiltered.sif', 'BINDyeast.sif']

5.3. Reference 21



py4cytoscape.collections.get_collection_name

get_collection_name(collection_suid=None, base_url='http://localhost:1234/v1')Get Collection Name.

Parameters

• collection_suid (SUID or None) – SUID of a collection (or None for “current”collection)


Returns the name of the collection associated with SUID

Return type str

Raises

• CyError – if no collection exists

• requests.exceptions.RequestException – if can’t connect to Cytoscape orCytoscape returns an error or SUID doesn’t exist

Examples

>>> get_collection_name()'galFiltered.sif'>>> get_collection_suid(851296)'galFiltered.sif'

py4cytoscape.collections.get_collection_networks

get_collection_networks(collection_suid=None, base_url='http://localhost:1234/v1')Get Collection Networks.

Parameters

• collection_suid (SUID or None) – SUID of a collection (or None for “current”collection)


Returns list of SUIDs for networks within the collection

Return type list

Raises


• requests.exceptions.RequestException – if can’t connect to Cytoscape orCytoscape returns an error or SUID doesn’t exist





Examples

>>> get_collection_name()'galFiltered.sif'>>> get_collection_suid(851296)'galFiltered.sif'

py4cytoscape.collections.get_collection_suid

get_collection_suid(network=None, base_url='http://localhost:1234/v1')Get Collection Suid.

Parameters

• network (SUID or str or None) – Network name or SUID of a network in thecollection


Returns the SUID of the collection containing the network

Return type int

Raises



Examples

>>> get_collection_suid()[851280]>>> get_collection_suid('current')[851280]>>> get_collection_suid(851296)[851280]>>> get_collection_suid('galFiltered.sif')[851280]

5.3.3 Commands

Functions for constructing any arbitrary CyREST API or Commands API method via standard GET, PUT, POST andDELETE protocols. These functions handle marshalling and unmarshalling of urls, parameters and returns so thathigher-level functions can work with Python-friendly arguments and returns.

I. CyREST API functions

II. Commands API functions

III. Internal functions

5.3. Reference 23



CyREST API

cyrest_delete([operation, parameters, . . . ]) Construct a query, make DELETE call and process theresult.

cyrest_get([operation, parameters, . . . ]) Construct a query, make GET call and process the result.cyrest_post([operation, parameters, body, . . . ]) Construct a query and body, make POST call and pro-

cess the result.cyrest_put([operation, parameters, body, . . . ]) Construct a query and body, make PUT call and process

the result.

py4cytoscape.commands.cyrest_delete

cyrest_delete(operation=None, parameters=None, base_url='http://localhost:1234/v1', re-quire_json=True)

Construct a query, make DELETE call and process the result.

Parameters

• operation (str) – A string to be converted to the REST query namespace

• parameters (dict) – A named list of values to be converted to REST query parameters


• require_json (bool) – True if only JSON is accepted as a response; otherwise, returnnon-JSON if response is non-JSON

Returns a dict if result was JSON; otherwise a string

Return type str or dict

Raises

• ValueError – if JSON is expected and response is not JSON


Examples

>>> cyrest_delete('networks/51/views', require_json=False) # deletes views for→˓network 51''>>> cyrest_delete('session') # deletes the current session{'message': 'New session created.'}




py4cytoscape.commands.cyrest_get

cyrest_get(operation=None, parameters=None, base_url='http://localhost:1234/v1', require_json=True)Construct a query, make GET call and process the result.

Parameters







Raises



Examples

>>> cyrest_get('gc', require_json=False) # starts Cytoscape garbage collection''>>> cyrest_get('version') # fetches CyREST version{'apiVersion': 'v1', 'cytoscapeVersion': '3.8.0'}

py4cytoscape.commands.cyrest_post

cyrest_post(operation=None, parameters=None, body=None, base_url='http://localhost:1234/v1', re-quire_json=True)

Construct a query and body, make POST call and process the result.

Parameters



• body (dict) – A named list of values to be converted to JSON





5.3. Reference 25




Raises



Examples

>>> cyrest_post('networks/51/views') # Add a view to a network{'networkViewSUID': '52'}>>> cyrest_post('commands/command/echo', body={'message': 'Hi there'}) # echo a→˓message{'data': ['Hi there'], 'errors': '[]}

py4cytoscape.commands.cyrest_put

cyrest_put(operation=None, parameters=None, body=None, base_url='http://localhost:1234/v1', re-quire_json=True)

Construct a query and body, make PUT call and process the result.

Parameters



• body (dict) – A named list of values to be converted to JSON





Raises



Examples

>>> cyrest_put('networks/views/currentNetworkView', body={'networkViewSUID': view}→˓) # Make a view the current view{'data': {}, 'errors': '[]}




Cytoscape Commands API

commands_get(cmd_string[, base_url]) Commands GET.commands_help([cmd_string, base_url]) Commands Help.commands_post(cmd[, base_url]) Commands POST.commands_run(cmd_string[, base_url]) Run a Command.

py4cytoscape.commands.commands_get

commands_get(cmd_string, base_url='http://localhost:1234/v1')Commands GET.

Using the same syntax as Cytoscape’s Command Line Dialog, this function converts a command string into aCyREST query URL, executes a GET request, and parses the result content into a list object.

Parameters

• cmd_string (str) – command


Returns a list of lines in the command result (omitting the “Finished” line at the end)

Return type list

Raises

• CyError – if command has an error


Examples

>>> commands_get('command sleep duration=5')[]>>> commands_get('apps status app="Network Merge"')['app: Network Merge, status: Installed']>>> commands_get('view')["Available commands for 'view':", 'create', 'destroy', 'export', 'fit content',→˓'fit selected', ...]

py4cytoscape.commands.commands_help

commands_help(cmd_string='help', base_url='http://localhost:1234/v1')Commands Help.

Using the same syntax as Cytoscape’s Command Line Dialog, this function returns a list of available commandsor args. Works with or without ‘help’ command prefix. Note that if you ask about a command that doesn’t haveany arguments, this function will run the command!

Parameters


5.3. Reference 27





Return type list

Raises



Examples

>>> commands_help('apps')['disable', 'enable', 'information', 'install', 'list available', 'list disabled',→˓ ...]

py4cytoscape.commands.commands_post

commands_post(cmd, base_url='http://localhost:1234/v1')Commands POST.

Using the same syntax as Cytoscape’s Command Line Dialog, this function converts a command string into aCyREST query URL, executes a POST request, and parses the result content into a dict object.

Parameters



Returns a structured command reply

Return type dict or list

Raises



Examples

>>> commands_post('apps status app="Network Merge"'){'appName': 'Network Merge', 'status': 'Installed'}>>> commands_post('apps list available')[{appName: 'CHAT', 'description': 'Identify contextually relevant hubs in→˓biological networks', 'details': ''},{'appName': 'AgilentLiteratureSearch', 'description': 'Mines scientific→˓literature to ... ', 'details': ''} ...]





py4cytoscape.commands.commands_run

commands_run(cmd_string, base_url='http://localhost:1234/v1')Run a Command.

Using the same syntax as Cytoscape’s Command Line Dialog, this function converts a command string into aCyREST query URL, executes a GET request, and parses the result content into a list object. Same as com-mandsGET.

Parameters




Return type list

Raises



Examples

>>> commands_run('session new destroyCurrentSession=true')[]

Cytoscape Commands

command_echo([variable_name, base_url]) Command Echo.command_open_dialog([base_url]) Command Open Dialog.command_pause([message, base_url]) Command Pause.command_quit([base_url]) Command Quit.command_run_file(file[, args, base_url]) Command Run File.command_sleep([duration, base_url]) Command Sleep.

py4cytoscape.commands.command_echo

command_echo(variable_name='*', base_url='http://localhost:1234/v1')Command Echo.

The echo command will display the value of the variable specified by the variableName argument, or all vari-ables if variableName is not provided.

Parameters

• variable_name (str) – The name of the variable to display. Default is to display allvariable values using “*”.

• base_url (str) – Ignore unless you need to specify a custom domain, port or version to

5.3. Reference 29



connect to the CyREST API. Default is http://localhost:1234 and the latest version of theCyREST API supported by this version of py4cytoscape.

Returns a list containing as single string containing the variable_name value

Return type list


Examples

>>> command_echo('Hi there')['Hi there']>>> command_echo()['*']

py4cytoscape.commands.command_open_dialog

command_open_dialog(base_url='http://localhost:1234/v1')Command Open Dialog.

The command line dialog provides a field to enter commands and view results. It also provides the help com-mand to display namespaces, commands, and arguments


Returns None


Examples

>>> command_open_dialog()

py4cytoscape.commands.command_pause

command_pause(message='', base_url='http://localhost:1234/v1')Command Pause.

The pause command displays a dialog with the text provided in the message argument and waits for the user toclick OK.

Parameters

• message (str) – Text to display in pause dialog


Returns {}






Return type dict


Examples

>>> command_pause(){}

py4cytoscape.commands.command_quit

command_quit(base_url='http://localhost:1234/v1')Command Quit.

This command causes Cytoscape to exit. It is typically used at the end of a script file


Returns {}

Return type dict


Examples

>>> command_quit(){}

py4cytoscape.commands.command_run_file

command_run_file(file, args=None, base_url='http://localhost:1234/v1')Command Run File.

The run command will execute a command script from the file pointed to by the file argument, which shouldcontain Cytoscape commands, one per line. Arguments to the script are provided by the args argument


Returns {}

Return type dict


5.3. Reference 31




Examples

>>> command_run_file('data/CommandScript.txt'){}

py4cytoscape.commands.command_sleep

command_sleep(duration=None, base_url='http://localhost:1234/v1')Command Sleep.

The sleep command will pause processing for a period of time as specified by duration seconds. It is typicallyused as part of a command script.

Parameters

• duration (float) – The time in seconds to sleep


Returns {}

Return type dict


Examples

>>> command_sleep(6){}

Swagger API-level Documentation

commands_api([base_url]) Open Swagger docs for CyREST Commands API.cyrest_api([base_url]) Open Swagger docs for CyREST API.

py4cytoscape.commands.commands_api

commands_api(base_url='http://localhost:1234/v1')Open Swagger docs for CyREST Commands API.

Opens swagger docs in default browser for a live instance of Commands available via CyREST.


Returns True

Return type bool






Examples

>>> commands_api() # loads Swagger CyREST Commands API into browserTrue

py4cytoscape.commands.cyrest_api

cyrest_api(base_url='http://localhost:1234/v1')Open Swagger docs for CyREST API.

Opens swagger docs in default browser for a live instance of CyREST operations.


Returns True

Return type bool


Examples

>>> cyrest_api() # loads Swagger CyREST API into browserTrue

5.3.4 CyNDEx

Functions for communicating with NDEx from within Cytoscape.

Read/Write

export_network_to_ndex(username, password,. . . )

Send a copy of a Cytoscape network to NDEx as a newsubmission.

import_network_from_ndex(ndex_id[, . . . ]) Import a network from the NDEx database into Cy-toscape.

update_network_in_ndex(username, password,. . . )

Update Network In NDEx.

5.3. Reference 33



py4cytoscape.cy_ndex.export_network_to_ndex

export_network_to_ndex(username, password, is_public, network=None, metadata=None,base_url='http://localhost:1234/v1')

Send a copy of a Cytoscape network to NDEx as a new submission.

Parameters

• username (str) – NDEx account username; required for private content

• password (str) – NDEx account password; required for private content

• is_public (bool) – Whether to make the network publicly accessible at NDEx.

• network (SUID or str or None) – Name or SUID of a network. Default is the“current” network active in Cytoscape.

• metadata (dict) – A list of structured information describing the network


Returns NDEx identifier externalId for new submission

Return type str

Raises

• CyError – if credentials or network are invalid


Examples

>>> export_network_to_ndex('userid', 'password', False)'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'>>> export_network_to_ndex('userid', 'password', False, network='galFiltered.sif')'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'

py4cytoscape.cy_ndex.import_network_from_ndex

import_network_from_ndex(ndex_id, username=None, password=None, access_key=None,base_url='http://localhost:1234/v1')

Import a network from the NDEx database into Cytoscape.

Parameters

• ndex_id (str) – Network externalId provided by NDEx. This is not the same as aCytoscape SUID.



• access_key (str) – NDEx accessKey; alternate acccess to private content






Returns SUID of imported network

Return type int

Raises

• CyError – if credentials, NDEx ID or access_key are invalid


Examples

>>> import_network_from_ndex(galFiltered_uuid, 'userid', 'password')52>>> import_network_from_ndex(galFiltered_uuid, access_key=test_key)52

py4cytoscape.cy_ndex.update_network_in_ndex

update_network_in_ndex(username, password, is_public, network=None, metadata=None,base_url='http://localhost:1234/v1')

Update Network In NDEx.

Update an existing network in NDEx, given a previously assoicaiated Cytoscape network, e.g., previously ex-ported to NDEx or imported from NDEx.

Parameters



• is_public (bool) – Whether to make the network publicly accessible at NDEx.




Returns NDEx identifier externalId for the updated submission

Return type str

Raises

• CyError – if credentials or network are invalid


5.3. Reference 35



Examples

>>> update_network_in_ndex('userid', 'password', False)'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'>>> update_network_in_ndex('userid', 'password', False, network='galFiltered.sif')'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'

Utility

get_network_ndex_id([network, base_url]) Get Network NDEx Id.

py4cytoscape.cy_ndex.get_network_ndex_id

get_network_ndex_id(network=None, base_url='http://localhost:1234/v1')Get Network NDEx Id.

Retrieve the NDEx externalId for a Cytoscape network, presuming it has already been exported to NDEx.

If the Cytoscape network is not associated with an NDEx network, the return value will be None.

Parameters




Returns NDEx identifier externalId or NULL

Return type str

Raises

• CyError – if network is invalid


Examples

>>> get_network_ndex_id()'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'>>> get_network_ndex_id(network='galFiltered.sif')'7bc2548c-9c93-11ea-aaef-0ac135e8bacf'




5.3.5 Cytoscape System

Functions for inspecting and managing apps for Cytoscape.

Resources

cytoscape_free_memory([base_url]) Manually call Java’s garbage collection System.gc() to free up unused memory.

cytoscape_memory_status([base_url]) Returns the memory resources of the server running Cy-toscape.

cytoscape_number_of_cores([base_url]) Returns the processor resources of the server runningCytoscape.

py4cytoscape.cytoscape_system.cytoscape_free_memory

cytoscape_free_memory(base_url='http://localhost:1234/v1')Manually call Java’s garbage collection System.gc() to free up unused memory.

This process happens automatically, but may be useful to call explicitly for testing or evaluation purposes.


Returns ‘Unused memory freed up.’

Return type str

Raises

• CyError – if can’t free memory


Examples

>>> cytoscape_free_memory()'Unused memory freed up.'

py4cytoscape.cytoscape_system.cytoscape_memory_status

cytoscape_memory_status(base_url='http://localhost:1234/v1')Returns the memory resources of the server running Cytoscape.


Returns {‘usedMemory’: <mem>, ‘freeMemory’: <mem>, ‘totalMemory’: <mem>, ‘maxMem-ory’: <mem>} where <mem> is a count of megabytes

Return type dict

5.3. Reference 37





Examples

>>> cytoscape_memory_status(){'usedMemory': 160, 'freeMemory': 1819, 'totalMemory': 1979, 'maxMemory': 5510}

py4cytoscape.cytoscape_system.cytoscape_number_of_cores

cytoscape_number_of_cores(base_url='http://localhost:1234/v1')Returns the processor resources of the server running Cytoscape.


Returns count of available CPUs

Return type int


Examples

>>> cytoscape_number_of_cores()4

System

cytoscape_api_versions([base_url]) Get the list of available CyREST API versions.cytoscape_ping([base_url]) Ping Cytoscapecytoscape_version_info([base_url]) Return the versions of the current Cytoscape and

CyREST API.

py4cytoscape.cytoscape_system.cytoscape_api_versions

cytoscape_api_versions(base_url='http://localhost:1234/v1')Get the list of available CyREST API versions.


Returns list of available API versions

Return type list






Examples

>>> cytoscape_api_versions()['v1']

py4cytoscape.cytoscape_system.cytoscape_ping

cytoscape_ping(base_url='http://localhost:1234/v1')Ping Cytoscape

Tests the connection to Cytoscape via CyREST and verifies that supported versions of Cytoscape and CyRESTAPI are loaded.


Returns None

Raises

• CyError – if error connecting to CyREST or version is unsupported


Examples

>>> cytoscape_ping()You are connected to Cytoscape!

py4cytoscape.cytoscape_system.cytoscape_version_info

cytoscape_version_info(base_url='http://localhost:1234/v1')Return the versions of the current Cytoscape and CyREST API.


Returns {‘apiVersion’: <version>, ‘cytoscapeVersion’: <version>}

Return type dict

Raises

• CyError – if error connecting to CyREST


5.3. Reference 39




Examples

>>> cytoscape_version_info(){'apiVersion': 'v1', 'cytoscapeVersion': '3.8.0'}

5.3.6 Exceptions

Error classes for py4cytoscape.

Exceptions

CyError

py4cytoscape.exceptions.CyError

exception CyError

5.3.7 Filters

Functions for working with FILTERS for the selection of nodes and edges in networks, including operations to importand export filters. In the Cytoscape user interface, filters are managed in the Select tab of the Control Panel.

Existing Filters

apply_filter([filter_name, hide, network, . . . ]) Run an existing filter by supplying the filter name.export_filters([filename, base_url]) Saves filters to file in JSON format.get_filter_list([base_url]) Retrieve list of named filters in current sessionimport_filters(filename[, base_url]) Loads filters from a file in JSON format.

py4cytoscape.filters.apply_filter

apply_filter(filter_name='Default filter', hide=False, network=None,base_url='http://localhost:1234/v1')

Run an existing filter by supplying the filter name.

Parameters

• filter_name (str) – Name of filter to apply. Default is “Default filter”.

• hide (bool) – Whether to hide filtered out nodes and edges. Default is FALSE. Ignoredif all nodes or edges are filtered out. This is an alternative to filtering for node and edgeselection.

• network (SUID or str or None) – Name or SUID of the network. Default is the“current” network active in Cytoscape.

• base_url (str) – Ignore unless you need to specify a custom domain, port or version toconnect to the CyREST API. Default is http://localhost:1234 and the latest version of the




CyREST API supported by this version of py4cytoscape.

Returns {‘nodes’: <node list>, ‘edges’: <edge list>} returns list of nodes and edges selected afterfilter executes

Return type dict

Raises

• CyError – if filter doesn’t exist


Examples

>>> apply_filter('degree filter 1x'){'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> apply_filter('degree filter 1x', hide=True, network='My Network'){'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}

See also:

unhide_all()

py4cytoscape.filters.export_filters

export_filters(filename='filters.json', base_url='http://localhost:1234/v1')Saves filters to file in JSON format.

Parameters

• filename (str) – Full path or path relavtive to current working directory, in addition tothe name of the file. Default is “filters.json”.


Returns {}

Return type dict


Examples

>>> export_filters() # Saves all filters in file 'filters.json'{}>>> export_filters('test.json') # Saves all filters in file 'test.json'{}>>> export_filters('test') # Saves all filters in file 'test.json'{}

5.3. Reference 41



py4cytoscape.filters.get_filter_list

get_filter_list(base_url='http://localhost:1234/v1')Retrieve list of named filters in current session


Returns returns list of available filter names

Return type list


Examples

>>> get_filter_list()['degree filter 1x', 'degree filter 2x']

py4cytoscape.filters.import_filters

import_filters(filename, base_url='http://localhost:1234/v1')Loads filters from a file in JSON format.

Adds filters to whatever filters already exist, and renames filters where names already exist. Also executes eachfilter.

Parameters

• filename (str) – Path and name of the filters file to load.


Returns {}

Return type dict


Examples

>>> import_filters('test.json') # Fetches filters in file 'test.json'{}>>> import_filters('test') # Fetches filters in file 'test'{}





New Filters

create_column_filter(filter_name, column,. . . )

Create Column Filter.

create_composite_filter(filter_name, fil-ter_list)

Combine filters to control node and edge selection basedon previously created filters.

create_degree_filter(filter_name, criterion) Create Degree Filter.

py4cytoscape.filters.create_column_filter

create_column_filter(filter_name, column, criterion, predicate, caseSensitive=False,anyMatch=True, type='nodes', hide=False, network=None,base_url='http://localhost:1234/v1')

Create Column Filter.

Create a filter to control node or edge selection. Works on columns of boolean, string, numeric and lists. Notethe unique restrictions for criterion and predicate depending on the type of column being filtered.

Parameters

• filter_name (str) – Name for new filter.

• column (str) – Table column to base filter upon.

• criterion (list, bool, str, int or float) – For boolean columns: Trueor False. For string columns: a string value, e.g., “hello”. If the predicate is REGEX thenthis can be a regular expression as accepted by the Java Pattern class (https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html). For numeric columns: If the predicateis BETWEEN or IS_NOT_BETWEEN then this is a two-element list of numbers, example:[1,5], otherwise a single number.

• predicate (str) – For boolean columns: IS, IS_NOT. For string columns: IS,IS_NOT, CONTAINS, DOES_NOT_CONTAIN, REGEX. For numeric columns:IS, IS_NOT, GREATER_THAN, GREATER_THAN_OR_EQUAL, LESS_THAN,LESS_THAN_OR_EQUAL, BETWEEN, IS_NOT_BETWEEN.

• caseSensitive (bool) – If string matching should be case sensitive. Default is FALSE.

• anyMatch (bool) – Only applies to List columns. If true then at least one element in thelist must pass the filter, if false then all the elements in the list must pass the filter. Defaultis TRUE.

• type (str) – Apply filter to “nodes” (default) or “edges”.





Return type dict

5.3. Reference 43

https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html

https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html



Raises

• CyError – if column doesn’t exist in the table named by type


Examples

>>> create_column_filter('myFilter', 'log2FC', [-1,1], "IS_NOT_BETWEEN") # filter→˓on numeric value log2FC{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'pValue', 0.05, "LESS_THAN") # Filter on→˓floating point column pValue{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'function', "kinase", "CONTAINS", False) #→˓Function on string column name{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'name', "^Y.*C$", "REGEX") # Filter on→˓string column name{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'isTarget', True , "IS") # Filter on boolean→˓column isTarget{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'isTarget', True , "IS", hide=True) # Filter→˓on boolean column isTarget{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', 'Betweenness', [300, 600] , "BETWEEN", type=→˓'edges') # Filter edges{'nodes': None, 'edges': [{'YPR119W (pd) YMR043W', 'YDR412W (pp) YPR119W'}]}

py4cytoscape.filters.create_composite_filter

create_composite_filter(filter_name, filter_list, type='ALL', hide=False, network=None,base_url='http://localhost:1234/v1')

Combine filters to control node and edge selection based on previously created filters.

Parameters


• filter_list (list) – List of names of filters to combine.

• type (str) – Type of composition, requiring ALL (default) or ANY filters to pass for finalnode and edge selection.








Return type dict

Raises

• CyError – if filter list contains less than one filter or has filters that don’t exist


Examples

>>> create_composite_filter('New Filter', ['degree filter 1x', 'degree filter 2x→˓']){'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_composite_filter('New Filter', ['degree filter 1x', 'column filter 10x→˓'], type='ANY', network="My network"){'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': [{'YPR119W (pd)→˓YMR043W', 'YDR412W (pp) YPR119W'}]}>>> create_composite_filter('New Filter', ['degree filter 1x', 'degree filter 2x→˓'], hide=True){'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}

py4cytoscape.filters.create_degree_filter

create_degree_filter(filter_name, criterion, predicate='BETWEEN', edge_type='ANY', hide=False,network=None, base_url='http://localhost:1234/v1')

Create Degree Filter.

Creates a filter to control node selection base on in/out degree.

Parameters


• criterion (list) – A two-element vector of numbers, example: [1,5].

• predicate (str) – BETWEEN (default) or IS_NOT_BETWEEN

• edgeType (str) – Type of edges to consider in degree count: ANY (default), UNDI-RECTED, INCOMING, OUTGOING, DIRECTED





Return type dict

5.3. Reference 45



Raises

• CyError – if criterion is not list of two values


Examples

>>> create_degree_filter('myFilter', [2, 5]) # filter on any nodes having between→˓2 and 5 edges{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_degree_filter('myFilter', [2, 5], predicate='IS_NOT_BETWEEN') # filter→˓for edges < 2 or > 5{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', [2, 5], edge_type='INCOMING') # filter for→˓between 2 and 5 incoming edges{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}>>> create_column_filter('myFilter', [2, 5], hide=True) # filter for between 2→˓and 5 edges, and hide them{'nodes': ['YDR395W', 'YLR362W', 'YPL248C', 'YGL035C'], 'edges': None}

5.3.8 Groups

Functions for working with GROUPS in Cytoscape.

Add/Remove Groups and Nodes

add_to_group(group_name[, nodes, . . . ]) Add the specified nodes and edges to the specifiedgroup.

create_group(group_name[, nodes, . . . ]) Create a group from the specified nodes.create_group_by_column(group_name[, col-umn, . . . ])

Create a group of nodes defined by a column value.

delete_group([groups, groups_by_col, . . . ]) Delete one or more groups, while leaving member nodesintact.

remove_from_group(group_name[, nodes, . . . ]) Remove the specified nodes and edges from the speci-fied group.

py4cytoscape.groups.add_to_group

add_to_group(group_name, nodes=None, nodes_by_col='SUID', edges=None, edges_by_col='SUID', net-work=None, base_url='http://localhost:1234/v1')

Add the specified nodes and edges to the specified group.

Parameters

• group_name (str) – Specifies the name used to identify the group

• nodes (list or str or None) – List of node SUIDs, names, other column values,or keyword: selected, unselected or all. Default is currently selected nodes.

• nodes_by_col (str) – name of node table column corresponding to provided nodes list.Default is ‘SUID’.



• edges (list or str or None) – List of edge SUIDs, names, other column values,or keyword: selected, unselected or all. Default is currently selected edges.

• edges_by_col (str) – name of edge table column corresponding to provided edges list.Default is ‘SUID’.



Returns {}

Return type dict

Raises

• CyError – if network name or SUID doesn’t exist


Examples

>>> add_to_group('Group 1', ['GDS1', 'SIP4', 'PDC1'], nodes_by_col='COMMON') #→˓add nodes by common name & all selected edges{}>>> add_to_group('Group 1') # add all selected nodes and edges{}>>> add_to_group('Group 1', ['GDS1', 'SIP4', 'PDC1'], nodes_by_col='COMMON',→˓edges=[]) # add all selected nodes and no edges{}>>> add_to_group('Group 1', nodes='unselected', edges='unselected') # add all→˓unselected nodes and edges{}

py4cytoscape.groups.create_group

create_group(group_name, nodes=None, nodes_by_col='SUID', network=None,base_url='http://localhost:1234/v1')

Create a group from the specified nodes.

Parameters

• group_name (str) – The name used to identify and optionaly label the group





5.3. Reference 47




Returns {‘group’: SUID} where SUID identifies the node corresponding to the group

Return type dict

Raises



Examples

>>> create_group('Group 1', ['GDS1', 'SIP4', 'PDC1'], nodes_by_col='COMMON') #→˓create group containing nodes by common name{'group': 95335}>>> create_group('Group 1') # create group containing all selected nodes{'group': 95335}>>> create_group('Group 1', []) # create group with no nodes{'group': 95335}>>> create_group('Group 1', nodes='unselected') # create group with all→˓unselected nodes{'group': 95335}

py4cytoscape.groups.create_group_by_column

create_group_by_column(group_name, column=None, value=None, network=None,base_url='http://localhost:1234/v1')

Create a group of nodes defined by a column value.

Parameters

• group_name (str) – The name used to identify and optionaly label the new group

• column (str) – The name or header of the Node Table column to use for selecting nodesto group

• value (str or int or float or bool) – The value in the column to use for se-lecting nodes to group



Returns {‘group’: group SUID} where the SUID identifies new group

Return type dict

Raises






Examples

>>> create_group_by_column('Group 1', 'Cluster', 'A'){'group': 95336}

py4cytoscape.groups.delete_group

delete_group(groups=None, groups_by_col='SUID', network=None, base_url='http://localhost:1234/v1')Delete one or more groups, while leaving member nodes intact.

Parameters

• groups (list or str or None) – all, selected, unselected. Default is the currentlyselected group.

• groups_by_col (str) – name of node table column corresponding to provided groupslist. Default is ‘SUID’.



Returns {‘groups’: [group SUIDs]} with the SUID for each deleted group in the list

Return type dict

Raises



Examples

>>> delete_group(['Group 1', 'Group 2'], groups_by_col='shared name') # delete→˓groups by name{groups:[7970, 7980]}>>> delete_group([7970]) # delete groups by SUID{groups:[7970]}>>> delete_group() # delete all selected groups{groups:[7970, 7980]}>>> delete_group(groups='all') # delete all groups{groups:[7970, 7980]}

Note: Group nodes are ungrouped but not deleted in Cytoscape 3.6.1

5.3. Reference 49



py4cytoscape.groups.remove_from_group

remove_from_group(group_name, nodes=None, nodes_by_col='SUID', edges=None,edges_by_col='SUID', network=None, base_url='http://localhost:1234/v1')

Remove the specified nodes and edges from the specified group.

Parameters

• group_name (str) – Specifies the name used to identify the group



• edges (list or str or None) – List of edge SUIDs, names, other column values,or keyword: selected, unselected or all. Default is currently selected edges.

• edges_by_col (str) – name of edge table column corresponding to provided edges list.Default is ‘SUID’.



Returns {}

Return type dict

Raises



Examples

>>> remove_from_group('Group 1', ['GDS1', 'SIP4', 'PDC1'], nodes_by_col='COMMON')→˓# remove nodes by common name & all their edges{}>>> remove_from_group('Group 1') # remove all selected nodes and edges{}>>> remove_from_group('Group 1', nodes=[], edges=[78565, 79565]) # remove edges→˓but not any nodes{}>>> remove_from_group('Group 1', nodes='unselected', edges='unselected') # remove→˓all unselected nodes and edges{}




Existing Groups

collapse_group([groups, network, base_url]) Replace the representation of all of the nodes and edgesin a group with a single node.

expand_group([groups, network, base_url]) Replaces the group node with member nodes for a set ofgroups.

get_group_info(group[, network, base_url]) Retrieve information about a group by name or identi-fier.

list_groups([network, base_url]) Retrieve a list of all group SUIDs in a network.

py4cytoscape.groups.collapse_group

collapse_group(groups=None, network=None, base_url='http://localhost:1234/v1')Replace the representation of all of the nodes and edges in a group with a single node.

Parameters

• groups (list or str) – List of group names or keywords: all, selected, unselected.Default is the currently selected group.



Returns {‘groups’: [List of SUIDs]} where SUID identifies the node corresponding to the groupthat was collapsed (even if it was already collapsed)

Return type dict

Raises

• CyError – if network name or SUID, or group name or SUID doesn’t exist


Examples

>>> collapse_group() # collapse all selected groups{'groups': [95335, 95336]}>>> collapse_group('all') # collapse all groups{'groups': [95335, 95336, 95337]}>>> collapse_group(['Group 1', 'Group 2']) # collapse 2 groups{'groups': [95335, 95336]}>>> collapse_group('Group 1,Group 2') # collapse 2 groups{'groups': [95335, 95336]}>>> collapse_group(['SUID:95335', 'SUID:95336']) # collapse 2 groups{'groups': [95335, 95336]}

5.3. Reference 51



py4cytoscape.groups.expand_group

expand_group(groups=None, network=None, base_url='http://localhost:1234/v1')Replaces the group node with member nodes for a set of groups.

Parameters

• groups (list or str) – List of group names or keywords: all, selected, unselected.Default is the currently selected group.



Returns {‘groups’: [List of SUIDs]} where SUID identifies the node corresponding to the groupthat was expanded (even if it was already expanded)

Return type dict

Raises

• CyError – if network name or SUID, or group name or SUID doesn’t exist


Examples

>>> expand_group() # expand all selected groups{'groups': [95335, 95336]}>>> expand_group('all') # expand all groups{'groups': [95335, 95336, 95337]}>>> expand_group(['Group 1', 'Group 2']) # expand 2 groups{'groups': [95335, 95336]}>>> expand_group('Group 1,Group 2') # expand 2 groups{'groups': [95335, 95336]}>>> expand_group(['SUID:95335', 'SUID:95336']) # expand 2 groups{'groups': [95335, 95336]}

py4cytoscape.groups.get_group_info

get_group_info(group, network=None, base_url='http://localhost:1234/v1')Retrieve information about a group by name or identifier.

Parameters

• group_name (str or SUID) – Group name or SUID.



Returns





{‘group’: SUID, ‘name’: name, ‘nodes’: [node SUIDs], ‘internalEdges’: [edge SUIDs], ‘externalEdges’: [edge SUIDs], ‘collapsed’: bool}where SUID identifies the node corresponding to the group, name is the name given tothe group at create time, node SUIDs is a list of nodes in the group, edge SUIDs is alist of edges within or reaching out of the group, and collapsed is True if the group iscollapsed.

Return type dict

Raises



Examples

>>> get_group_info('group 1'){'group': 95335,'name': 'group 1','nodes': [94214, 94038, 94122],'internalEdges': [],'externalEdges': [94450, 94564, 94403, 94362, 94506, 94537],'collapsed': False}>>> get_group_info(95335, network='My Network'){'group': 95335,'name': 'group 1','nodes': [94214, 94038, 94122],'internalEdges': [],'externalEdges': [94450, 94564, 94403, 94362, 94506, 94537],'collapsed': False}

py4cytoscape.groups.list_groups

list_groups(network=None, base_url='http://localhost:1234/v1')Retrieve a list of all group SUIDs in a network.

Parameters



Returns {groups: [SUID list]} as list of SUIDs for group nodes

Return type dict

Raises



5.3. Reference 53



Examples

>>> list_groups(){'groups': [94214, 94038, 94122]}

5.3.9 Layouts

Functions for performing LAYOUTS in addition to getting and setting layout properties.

I. Perform layout functions

II. Get layout properties

III. Set layout properties

Perform Layout

bundle_edges([network, base_url]) Apply edge bundling to the network specified.clear_edge_bends([network, base_url]) Clear all edge bends created from edge bundling.layout_copycat(source_network, target_network) Copy a layout from one network to another.layout_network([layout_name, network,base_url])

Apply a layout to a network.

py4cytoscape.layouts.bundle_edges

bundle_edges(network=None, base_url='http://localhost:1234/v1')Apply edge bundling to the network specified.

Edge bundling is executed with default parameters; optional parameters are not supported.

Parameters

• network (SUID or str or None) – Name or SUID of the network; default is “cur-rent” network.


Returns {‘message’: ‘Edge bundling success.’}

Return type dict

Raises

• CyError – if layout_name is invalid





Examples

>>> bundle_edges() # Bundle edges in current network{'message': 'Edge bundling success.'}>>> bundle_edges('yeastHighQuality.sif') # Bundle edges in named network{'message': 'Edge bundling success.'}

py4cytoscape.layouts.clear_edge_bends

clear_edge_bends(network=None, base_url='http://localhost:1234/v1')Clear all edge bends created from edge bundling.

Parameters



Returns {‘message’: ‘Clear all edge bends success.’}

Return type dict

Raises



Examples

>>> clear_edge_bends() # Clear edge bends in current network{'message': 'Edge bundling success.'}>>> clear_edge_bends('yeastHighQuality.sif') # Clear edge bends in named network{'message': 'Edge bundling success.'}

py4cytoscape.layouts.layout_copycat

layout_copycat(source_network, target_network, source_column='name', target_column='name',grid_unmapped=True, select_unmapped=True, base_url='http://localhost:1234/v1')

Copy a layout from one network to another.

Sets the coordinates for each node in the target network to the coordinates of a matching node in the sourcenetwork. Optional parameters such as gridUnmapped and selectUnmapped determine the behavior oftarget network nodes that could not be matched.

Parameters

• source_network (SUID or str or None) – Name of the network to get node co-ordinates from; default is “current” network. If an SUID is provided, the correspondingnetwork name is used.

5.3. Reference 55



• target_network (SUID or str or None) – Name of the network to apply coor-dinates to; default is “current” network. If an SUID is provided, the corresponding networkname is used.

• source_column (str) – The name of column in the source_network node table used tomatch nodes; default is ‘name’

• target_column (str) – The name of column in the target_network node table used tomatch nodes; default is ‘name’

• grid_unmapped (bool) – If this is set to True, any nodes in the target network that couldnot be matched to a node in the source network will be laid out in a grid; default is True

• select_unmapped (bool) – If this is set to True, any nodes in the target network thatcould not be matched to a node in the source network will be selected in the target network;default is True


Returns {‘mappedNodeCount’: 330, ‘unmappedNodeCount’: 0} containing count of nodes coordi-nates modified

Return type dict

Raises

• CyError – if source_network, target_network, source_column or target_column are in-valid


Examples

>>> layout_copycat('galFiltered.sif', galFiltered.sif_1){'mappedNodeCount': 330, 'unmappedNodeCount': 0}>>> layout_copycat('galFiltered.sif', galFiltered.sif_1, source_column='shared→˓name', target_column='shared name'){'mappedNodeCount': 330, 'unmappedNodeCount': 0}

py4cytoscape.layouts.layout_network

layout_network(layout_name=None, network=None, base_url='http://localhost:1234/v1')Apply a layout to a network.

Run getLayoutNames to list available layouts.

Parameters

• layout_name (str) – Name of the layout (with optional parameters). If not specified,then the preferred layout set in the Cytoscape UI is applied.






Returns {} empty

Return type dict

Raises



Examples

>>> layout_network() # Layout current network using default layout{}>>> layout_network('force-directed') # Layout current network using force-→˓directed layout{}>>> layout_network('grid', 'yeastHighQuality.sif') # layout named network using→˓grid layout{}

Layout Properties

get_layout_name_mapping([base_url]) Get Layout Name Mapping.get_layout_names([base_url]) Retrieve the names of the currently supported layout al-

gorithms.get_layout_property_names(layout_name[,. . . ])

Returns a list of the tunable properties for the specifiedlayout.

get_layout_property_type(layout_name, . . . [,. . . ])

Returns the type of one of the tunable properties (prop-erty_name) for the specified layout.

get_layout_property_value(layout_name,. . . )

Returns the appropriately typed value of the specifiedtunable property for the specified layout.

set_layout_properties(layout_name, . . . [,. . . ])

Sets the specified properties for the specified layout.

py4cytoscape.layouts.get_layout_name_mapping

get_layout_name_mapping(base_url='http://localhost:1234/v1')Get Layout Name Mapping.

The Cytoscape ‘Layout’ menu lists many layout algorithms, but the names presented there are different fromthe names by which these algorithms are known to `layout_network` method. This method returns anamed list in which the names are from the GUI, and the values identify the names you must use to choose analgorithms in the programmatic interface.


5.3. Reference 57




Returns {gui-layout-name: layout_name, . . . }

Return type dict


Examples

>>> get_layout_name_mapping(){'Attribute Circle Layout': 'attribute-circle', 'Stacked Node Layout': 'stacked-→˓node-layout' ...}

py4cytoscape.layouts.get_layout_names

get_layout_names(base_url='http://localhost:1234/v1')Retrieve the names of the currently supported layout algorithms.

These may be used in subsequent calls to the layout_network function.


Returns a list of layout names as strings

Return type list


Examples

>>> get_layout_names()['attribute-circle', 'stacked-node-layout', 'degree-circle', 'circular',→˓'attributes-layout', 'kamada-kawai', 'force-directed', 'cose', 'grid',→˓'hierarchical', 'fruchterman-rheingold', 'isom']

py4cytoscape.layouts.get_layout_property_names

get_layout_property_names(layout_name, base_url='http://localhost:1234/v1')Returns a list of the tunable properties for the specified layout.

Run getLayoutNames to list available layouts

Parameters

• layout_name (str) – Name of the layout


Returns strings naming layout parameters

Return type list





Raises requests.exceptions.RequestException – if layout_name is invalid or can’tconnect to Cytoscape or Cytoscape returns an error

Examples

>>> get_layout_property_names('force-directed')['numIterations', 'defaultSpringCoefficient', 'defaultSpringLength',→˓'defaultNodeMass', 'isDeterministic', 'singlePartition']

py4cytoscape.layouts.get_layout_property_type

get_layout_property_type(layout_name, property_name, base_url='http://localhost:1234/v1')Returns the type of one of the tunable properties (property_name) for the specified layout.

Run getLayoutNames to list available layouts. Run getLayoutPropertyNames to list properties perlayout.

Parameters


• property_name (str) – Name of the property



Return type list

Raises

• KeyError – if property_name is invalid

• requests.exceptions.RequestException – if layout_name is invalid or can’tconnect to Cytoscape or Cytoscape returns an error

Examples

>>> get_layout_property_names('force-directed','defaultSpringLength')"double"

py4cytoscape.layouts.get_layout_property_value

get_layout_property_value(layout_name, property_name, base_url='http://localhost:1234/v1')Returns the appropriately typed value of the specified tunable property for the specified layout.


Parameters


• property_name (str) – Name of the property

5.3. Reference 59





Return type list

Raises

• KeyError – if property_name is invalid

• requests.exceptions.RequestException – if layout_name is invalid or can’tconnect to Cytoscape or Cytoscape returns an error

Examples

>>> getLayoutPropertyValue('force-directed','defaultSpringLength')50

py4cytoscape.layouts.set_layout_properties

set_layout_properties(layout_name, properties_dict, base_url='http://localhost:1234/v1')Sets the specified properties for the specified layout.

Unmentioned properties are left unchanged.


Parameters


• properties_dict (dict) – List of one or more property=value pairs


Returns

’‘

Return type str

Raises requests.exceptions.RequestException – if layout_name is invalid or can’tconnect to Cytoscape or Cytoscape returns an error





Examples

>>> set_layout_properties('force-directed', {'defaultSpringLength': 50,→˓'defaultSpringCoefficient': 6E-01})''

5.3.10 Networks

Basic Networks

Functions for NETWORK management and retrieving information on networks, nodes and edges. Includes all func-tions that result in the creation of a new network in Cytoscape, in addition to funcitons that extract network modelsinto other useful objects.

I. General network functions

II. General node functions

III. General edge functions

IV. Network creation

V. Network extraction

VI. Internal functions

Note: Go to network_selection.py for all selection-related functions

Nodes

add_cy_nodes(node_names[, . . . ]) Add one or more nodes to a Cytoscape network.get_all_nodes([network, base_url]) Retrieve the names of all the nodes in the network.get_first_neighbors([node_names, . . . ]) Returns a non-redundant list of first neighbors of the

supplied list of nodes or current node selection.get_node_count([network, base_url]) Reports the number of nodes in the network.

py4cytoscape.networks.add_cy_nodes

add_cy_nodes(node_names, skip_duplicate_names=True, network=None,base_url='http://localhost:1234/v1')

Add one or more nodes to a Cytoscape network.

Parameters

• node_names (list or None) – A list of node names

• skip_duplicate_names (bool) – Skip adding a node if a node with the same nameis already in the network. If FALSE then a duplicate node (with a unique SUID) will beadded.

• network (SUID or str or None) – Name or SUID of a network or view. Default isthe “current” network active in Cytoscape.

5.3. Reference 61



Returns A list of named lists of name and SUID for each node added.

Return type list

Raises



Examples

>>> add_cy_nodes(['newnode1', 'newnode2'], skip_duplicate_names=False)[{"name": "newnode1", "SUID": 1459}, {"name": "newnode2", "SUID": 1460}]>>> add_cy_nodes(['newnode2', 'newnode3'], skip_duplicate_names=True)[{"name": "newnode3", "SUID": 1460}]

py4cytoscape.networks.get_all_nodes

get_all_nodes(network=None, base_url='http://localhost:1234/v1')Retrieve the names of all the nodes in the network.

Parameters



Returns a list of nodes in the network

Return type list

Raises

• ValueError – if server response has no JSON







Examples

>>> get_all_nodes()['YDL194W', 'YDR277C', 'YBR043C', ... ]

py4cytoscape.networks.get_first_neighbors

get_first_neighbors(node_names=None, as_nested_list=False, network=None,base_url='http://localhost:1234/v1')

Returns a non-redundant list of first neighbors of the supplied list of nodes or current node selection.

Parameters

• node_names (str or list or None) – A list of node names from the namecolumn of the node table. Default is currently selected nodes.

• as_nested_list (bool) – Whether to return lists of neighbors per query node.



Returns

deduped list of nodes neighboring specified nodes. If as_nested_list parameter is True, a listof neighbor node lists, one per specified node

Return type list

Raises

• CyError – if network name or SUID doesn’t exist, if no nodes are selected, or if nodedoesn’t exist


Examples

>>> get_first_neighbors(node_names = None, as_nested_list=True)[['YBR020W', ['YGL035C', 'YOL051W', 'YPL248C', 'YML051W']], ['YGL035C', ['YLR044C→˓', 'YLR377C', ...]], ...]>>> get_first_neighbors(['YBR020W', 'YGL035C'], as_nested_list=False)['YGL035C', 'YOL051W', 'YPL248C', 'YML051W', 'YLR044C', 'YLR377C', 'YIL162W', ...→˓]>>> get_first_neighbors('YBR020W', as_nested_list=False)['YGL035C', 'YOL051W', 'YPL248C', 'YML051W']

See also:

select_nodes(), select_first_neighbors()

5.3. Reference 63



py4cytoscape.networks.get_node_count

get_node_count(network=None, base_url='http://localhost:1234/v1')Reports the number of nodes in the network.

Parameters



Returns count of nodes in network.

Return type int

Raises




Examples

>>> get_node_count()6>>> get_node_count(52)6>>> get_node_count('galFiltered.sif')6

Edges

add_cy_edges(source_target_list[, . . . ]) Add one or more edges to a Cytoscape network by list-ing source and target node pairs.

get_all_edges([network, base_url]) Retrieve the names of all the edges in the network.get_edge_count([network, base_url]) Reports the number of the edges in the network.get_edge_info(edges[, network, base_url]) Returns source, target and edge table row values.

py4cytoscape.networks.add_cy_edges

add_cy_edges(source_target_list, edge_type='interacts with', directed=False, network=None,base_url='http://localhost:1234/v1')

Add one or more edges to a Cytoscape network by listing source and target node pairs.

Parameters

• source_target_list (list or list of lists) – Source and target node pairs

• edgeType (str) – The type of interaction. Default is ‘interacts with’.




• directed (bool) – Indicates whether interactions are directed. Default is FALSE.



Returns A list of dicts for each edge (SUID, source, target) added.

Return type list of dicts

Raises



Examples

>>> add_cy_edges(['YLR075W', 'YKL028W'])[{'SUID': 2884, 'source': 1552, 'target': 1698}]>>> add_cy_edges([['YKL028W', 'YJR066W'], ['YJR066W', 'YLR452C'], ['YGR046W',→˓'YLR452C']])[{'SUID': 2886, 'source': 1698, 'target': 1645}, {'SUID': 2887, 'source': 1645,→˓'target': 1534} ...]

py4cytoscape.networks.get_all_edges

get_all_edges(network=None, base_url='http://localhost:1234/v1')Retrieve the names of all the edges in the network.

Parameters



Returns a list of edges in the network

Return type list

Raises




5.3. Reference 65




Examples

>>> get_all_edges()['YDR277C (pp) YDL194W', 'YDR277C (pp) YJR022W', 'YPR145W (pp) YMR117C', ...]

py4cytoscape.networks.get_edge_count

get_edge_count(network=None, base_url='http://localhost:1234/v1')Reports the number of the edges in the network.

Parameters



Returns count of edges in network.

Return type int

Raises




Examples

>>> get_edge_count()6>>> get_edge_count(52)6>>> get_edge_count('galFiltered.sif')6

py4cytoscape.networks.get_edge_info

get_edge_info(edges, network=None, base_url='http://localhost:1234/v1')Returns source, target and edge table row values.

Parameters

• edges (list) – list of SUIDs or names of edges, i.e., values in the “name” column. Canalso input single edge.







Returns list of dicts describing each edge

Return type list of dicts

Raises




Examples

>>> get_edge_info('YDR277C (pp) YDL194W')[{'source': 2919, 'target': 2918, 'SUID': 3248, 'shared name': 'YDR277C (pp)→˓YDL194W','shared interaction': 'pp', 'name': 'YDR277C (pp) YDL194W', 'selected': False,'interaction': 'pp', 'EdgeBetweenness': 496.0}]

>>> get_edge_info(['YDR277C (pp) YDL194W', 'YDR277C (pp) YJR022W'])[{'source': 2919, 'target': 2918, 'SUID': 3248, 'shared name': 'YDR277C (pp)→˓YDL194W','shared interaction': 'pp', 'name': 'YDR277C (pp) YDL194W', 'selected': False,'interaction': 'pp', 'EdgeBetweenness': 496.0},

{'source': 2919, 'target': 3220, 'SUID': 3249, 'shared name': 'YDR277C (pp)→˓YJR022W','shared interaction': 'pp', 'name': 'YDR277C (pp) YJR022W', 'selected': False,'interaction': 'pp', 'EdgeBetweenness': 988.0}]

Notes: This function is kinda slow. It takes approximately 70ms per edge to return a result, e.g., 850 edges willtake one minute.

Network Management

clone_network([network, base_url]) Makes a copy of a Cytoscape Network with all of itsedges and nodes.

create_subnetwork([nodes, nodes_by_col, . . . ]) Copies a subset of nodes and edges into a newly createdsubnetwork.

delete_all_networks([base_url]) Delete all networks from the current Cytoscape session.delete_network([network, base_url]) Delete a network from the current Cytoscape session.get_network_count([base_url]) Get the number of Cytoscape networks in the current

Cytoscape session.get_network_list([base_url]) Returns the list of Cytoscape network names in the cur-

rent Cytoscape session.get_network_name([suid, base_url]) Get the name of a network.get_network_suid([title, base_url]) Get the SUID of a network.rename_network(title[, network, base_url]) Sets a new name for a network.set_current_network([network, base_url]) Selects the given network as “current”.

5.3. Reference 67


py4cytoscape.networks.clone_network

clone_network(network=None, base_url='http://localhost:1234/v1')Makes a copy of a Cytoscape Network with all of its edges and nodes.

Parameters



Returns The SUID of the new network

Return type int

Raises




Examples

>>> clone_network()1477

py4cytoscape.networks.create_subnetwork

create_subnetwork(nodes=None, nodes_by_col='SUID', edges=None, edges_by_col='SUID',exclude_edges=False, subnetwork_name=None, network=None,base_url='http://localhost:1234/v1')

Copies a subset of nodes and edges into a newly created subnetwork.

Parameters

• nodes (list) – list of node names or keyword: selected, unselected or all. Default iscurrently selected nodes.

• nodes_by_col (str) – name of node table column corresponding to provided nodes list;default is ‘SUID’

• edges (list) – list of edge names or keyword: selected, unselected or all. Default iscurrently selected edges.

• edges_by_col (str) – name of edge table column corresponding to provided edges list;default is ‘SUID’

• exclude_edges (bool) – whether to exclude connecting edges; default is FALSE

• subnetwork_name (str) – name of new subnetwork to be created; default is to add anumbered suffix to source network name






Returns The SUID of the new subnetwork

Return type int

Raises




Examples

>>> create_subnetwork(nodes='all') # choose all selected and unselected nodes1477>>> create_subnetwork(edges='selected') # choose only nodes whose edges are→˓selected, and include those edges1477>>> create_subnetwork(nodes=['RAP1', 'HIS4', 'PDC1', 'RPL18A'], nodes_by_col=→˓'COMMON', subnetwork_name=base_name+'xx')

1477

py4cytoscape.networks.delete_all_networks

delete_all_networks(base_url='http://localhost:1234/v1')Delete all networks from the current Cytoscape session.


Returns

’‘

Return type str


Examples

>>> delete_all_networks()

5.3. Reference 69




py4cytoscape.networks.delete_network

delete_network(network=None, base_url='http://localhost:1234/v1')Delete a network from the current Cytoscape session.

Parameters



Returns

’‘

Return type str

Raises



Examples

>>> delete_network() # delete the current network>>> delete_network(22752) # delete network having SUID>>> delete_network('galFiltered.sif') # delete network having name

py4cytoscape.networks.get_network_count

get_network_count(base_url='http://localhost:1234/v1')Get the number of Cytoscape networks in the current Cytoscape session.


Returns count of networks

Return type int

Raises







Examples

>>> get_network_count()3

py4cytoscape.networks.get_network_list

get_network_list(base_url='http://localhost:1234/v1')Returns the list of Cytoscape network names in the current Cytoscape session.


Returns network names

Return type list

Raises



Examples

>>> get_network_list()['yeastHighQuality.sif', 'galFiltered.sif']

py4cytoscape.networks.get_network_name

get_network_name(suid=None, base_url='http://localhost:1234/v1')Get the name of a network.

Parameters

• suid (SUID or str or None) – SUID of the network; default is current network. Ifa name is provided, then it is validated and returned.


Returns network name

Return type str

Raises




5.3. Reference 71




Examples

>>> get_network_name() # get name of current networkgalFiltered.sif>>> get_network_name(22752) # get name of network having SUIDgalFiltered.sif>>> get_network_name('galFiltered.sif') # verify that current network is→˓galFiltered.sifgalFiltered.sif

Notes

Together with getNetworkSuid, this function attempts to handle all of the multiple ways we support networkreferencing (e.g., title, SUID, ‘current’, and NULL). These functions are then used by all other functions thattake a “network” argument.

py4cytoscape.networks.get_network_suid

get_network_suid(title=None, base_url='http://localhost:1234/v1')Get the SUID of a network.

Parameters

• suid (SUID or str or None) – Name of the network; default is “current” network.If an SUID is provided, then it is validated and returned.


Returns network SUID

Return type int

Raises




Examples

>>> get_network_suid() # get SUID of current network22752>>> get_network_suid('galFiltered.sif') # get SUID of network having name22752>>> get_network_suid(22752) # verify that current network has SUID 2275222752




Notes

Together with getNetworkSuid, this function attempts to handle all of the multiple ways we support networkreferencing (e.g., title, SUID, ‘current’, and NULL). These functions are then used by all other functions thattake a “network” argument.

py4cytoscape.networks.rename_network

rename_network(title, network=None, base_url='http://localhost:1234/v1')Sets a new name for a network.

Duplicate network names are not allowed

Parameters

• title (str) – New name for the network

• network (SUID or str or None) – name or SUID of the network that you want torename; default is “current” network


Returns server JSON response

Return type dict

Raises




Examples

>>> rename_network('renamed network') # changes "current" network's name to→˓"renamed network"{'network': 22752, 'title': 'renamed network'}>>> rename_network('renamed network', 'MyNetwork') # changes network named→˓'MyNetwork' to be named "renamed network"{'network': 22752, 'title': 'renamed network'}>>> rename_network('renamed network', 1502) # sets network having SUID 1502 to be→˓named "renamed network"{'network': 1502, 'title': 'renamed network'}

5.3. Reference 73



py4cytoscape.networks.set_current_network

set_current_network(network=None, base_url='http://localhost:1234/v1')Selects the given network as “current”.

Parameters

• network (SUID or str or None) – Network name or SUID of the network that youwant set as current


Returns {} (empty dict)

Return type dict

Raises




Examples

>>> set_current_network() # sets current network to current{}>>> set_current_network('MyNetwork') # sets network named 'MyNetwork' as current{}>>> set_current_network(1502) # sets network having SUID 1502 as current{}

Import/Export

create_igraph_from_network([network,base_url])

Create an igraph network from a Cytoscape network.

create_network_from_data_frames([nodes,. . . ])

Create a network from data frames.

create_network_from_igraph(igraph[, title,. . . ])

Create a Cytoscape network from an igraph network.

create_network_from_networkx(netx[, title,. . . ])

Create a Cytoscape network from a NetworkX graph.

create_networkx_from_network([network,base_url])

Return the Cytoscape network as a networkx multi-di-graph.

export_network([filename, type, network, . . . ]) Export a network to one of mulitple file formats.import_network_from_file([file, base_url]) Loads a network from specified file.




py4cytoscape.networks.create_igraph_from_network

create_igraph_from_network(network=None, base_url='http://localhost:1234/v1')Create an igraph network from a Cytoscape network.

Notes

Takes a Cytoscape network and generates data frames for vertices and edges to send to thegraph_from_data_frame function. Nodes and edges from the Cytoscape network will be translated into ver-tices and edges in igraph. Associated table columns will also be passed to igraph as vertex and edge attributes.All networks are implicitly modeled as directed in Cytoscape. Round-trip conversion of an undirected net-work in igraph via createNetworkFromIgraph to Cytoscape and back to igraph will result in a directednetwork.

Parameters



Returns The new igraph object

Return type igraph

Raises




Examples

>>> create_igraph_from_network()IGRAPH DN-- 330 359 --+ attr: AverageShortestPathLength (v), BetweennessCentrality (v), COMMON (v),ClosenessCentrality (v), ClusteringCoefficient (v), Degree (v), Eccentricity(v), IsSingleNode (v), NeighborhoodConnectivity (v), NumberOfDirectedEdges(v), NumberOfUndirectedEdges (v), PartnerOfMultiEdgedNodePairs (v),Radiality (v), SelfLoops (v), Stress (v), TopologicalCoefficient (v),degree.layout (v), gal1RGexp (v), gal1RGsig (v), gal4RGexp (v), gal4RGsig(v), gal80Rexp (v), gal80Rsig (v), isExcludedFromPaths (v), name (v),selected (v), shared name (v), EdgeBetweenness (e), interaction (e), name(e), selected (e), shared interaction (e), shared name (e), source (e),target (e)

+ edges (vertex names):YML064C->YLR284C, YML064C->YHR198C, YKL074C->YGL035C, YDL081C->YLR340W,...

See also:

create_network_from_data_frames(), create_network_from_igraph()

5.3. Reference 75



py4cytoscape.networks.create_network_from_data_frames

create_network_from_data_frames(nodes=None, edges=None, title='From dataframe',collection='My Dataframe Network Collection',base_url='http://localhost:1234/v1', *, node_id_list='id',source_id_list='source', target_id_list='target', interac-tion_type_list='interaction')

Create a network from data frames.

Takes data frames for nodes and edges, as well as naming parameters to generate the JSON data format requiredby the “networks” POST operation via CyREST. Returns the network.suid and applies the preferred layout setin Cytoscape preferences.

Notes

nodes should contain a column of character strings named: id. This name can be overridden by the arg:node_id_list. Additional columns are loaded as node attributes. edges should contain columns of char-acter strings named: source, target and interaction. These names can be overridden by args: source_id_list,target_id_list, interaction_type_list. Additional columns are loaded as edge attributes. The interaction listcan contain a single value to apply to all rows; and if excluded altogether, the interaction type will be set to“interacts with”. NOTE: attribute values of types (num) will be imported as (Double); (int) as (Integer); (chr) as(String); and (logical) as (Boolean). (Lists) will be imported as (Lists) in CyREST v3.9+.

Note that the extra id column is created in the node table because the id column is mandatory in the cytoscape.jsformat, which is what is sent to Cytoscape.

Parameters

• nodes (DataFrame) – see details and examples below; default NULL to derive nodesfrom edge sources and targets

• edges (DataFrame) – see details and examples below; default NULL for disconnectedset of nodes

• title (str) – network name

• collection (str) – network collection name


• * –

• node_id_list (str) – Name of column in nodes containing node id

• source_id_list (str) – Name of column in edges containing source node name

• target_id_list (str) – Name of column in edges containing target node name

• interaction_type_list (str) – Name of column in edges containing interactionname


Return type int

Raises







Examples

>>> node_data = {'id':["node 0","node 1","node 2","node 3"],>>> 'group':["A","A","B","B"],>>> 'score':[20,10,15,5]}>>> nodes = df.DataFrame(data=node_data, columns=['id', 'group', 'score'])>>> edge_data = {'source':["node 0","node 0","node 0","node 2"],>>> 'target':["node 1","node 2","node 3","node 3"],>>> 'interaction':["inhibits","interacts","activates","interacts"],>>> 'weight':[5.1,3.0,5.2,9.9]}>>> edges = df.DataFrame(data=edge_data, columns=['source', 'target', 'interaction→˓', 'weight'])>>>>>> create_network_from_data_frames(nodes, edges, title='From node & edge→˓dataframe')1477

py4cytoscape.networks.create_network_from_igraph

create_network_from_igraph(igraph, title='From igraph', collection='My Igraph Network Collec-tion', base_url='http://localhost:1234/v1')

Create a Cytoscape network from an igraph network.

Takes an igraph network and generates data frames for nodes and edges to send to the createNetwork function.Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Notes

Vertices and edges from the igraph network will be translated into nodes and edges in Cytoscape. Associatedattributes will also be passed to Cytoscape as node and edge table columns. Note: undirected networks will beimplicitly modeled as directed in Cytoscape. Conversion back via createIgraphFromNetwork will resultin a directed network. Also note: igraph attributes of type “other” denoted by “x” are converted to “String” inCytoscape.

Note that the extra id column is created in the node table because the id column is mandatory in the cytoscape.jsformat, which is what is sent to Cytoscape.

Parameters

• igraph (igraph) – igraph network object





Return type int

Raises

5.3. Reference 77




• KeyError – igraph network doesn’t contain required node or edge attributes



Examples

>>> g = ig.Graph()>>> g.add_vertices(3)>>> g.vs['name'] = ['RAP1', 'HIS4', 'HIS3']>>> g.add_edges([(0, 1), (1, 2)])>>> g.es['source'] = [g.vs[0]['name'], g.vs[1]['name']]>>> g.es['target'] = [g.vs[1]['name'], g.vs[2]['name']]>>> g.es['interaction'] = ['enhances', 'inhibits']>>> create_network_from_igraph(g, 'new graph', 'my collection')138775

See also:

create_network_from_data_frames(), create_igraph_from_network()

py4cytoscape.networks.create_network_from_networkx

create_network_from_networkx(netx, title='From networkx', collection='My NetworkX Network Col-lection', base_url='http://localhost:1234/v1')

Create a Cytoscape network from a NetworkX graph.

Parameters

• netx (MultiDiGraph) – networkx MultiDiGraph object




Returns {‘networkSUID’: 31766}

Return type Dict





Examples

>>> n = create_network_from_networkx(netx){'networkSUID': 31766}>>> n = create_network_from_networkx(netx, 'Cool Networkx', 'Collection of Cool→˓Networks'){'networkSUID': 31766}

See also:

create_networkx_from_network()

py4cytoscape.networks.create_networkx_from_network

create_networkx_from_network(network=None, base_url='http://localhost:1234/v1')Return the Cytoscape network as a networkx multi-di-graph.

Parameters



Returns The new networkx object

Return type MultiDiGraph

Raises



Examples

>>> n = create_networkx_from_network(network='galFiltered.sif')>>> print(nx.info(n))Name:Type: MultiDiGraphNumber of nodes: 330Number of edges: 359Average in degree: 1.0879Average out degree: 1.0879

See also:

create_network_from_networkx()

5.3. Reference 79



py4cytoscape.networks.export_network

export_network(filename=None, type='SIF', network=None, base_url='http://localhost:1234/v1')Export a network to one of mulitple file formats.

Parameters

• filename (str) – Full path or path relavtive to current working directory, in addition tothe name of the file. Extension is automatically added based on the type argument. Ifblank, then the current network name is used.

• type (str) – File type. SIF (default), CX, cyjs, graphML, NNF, xGMML.



Returns server JSON response

Return type dict

Raises



Examples

>>> export_network('/path/filename','SIF'){ 'data': {'file': 'C:\Users\CyDeveloper\xx'}, 'errors': [] }

py4cytoscape.networks.import_network_from_file

import_network_from_file(file=None, base_url='http://localhost:1234/v1')Loads a network from specified file.

Parameters

• file (str) – Name of file in any of the supported formats (e.g., SIF, GML, xGMML, etc).If None, a demo network file in SIF format is loaded.


Returns {“networks”: [network suid], “views”: [suid for views]} where networks and views listshave length 1

Return type dict

Raises

• CyError – if file cannot be found or loaded






Examples

>>> import_network_from_file() # import demo network{'networks': [131481], 'views': [131850]}>>> import_network_from_file('data/yeastHighQuality.sif'){'networks': [131481], 'views': [131850]}

Network Selection

Functions for working with SELECTIONS of nodes and edges in networks, including operations that perform selectionand rely on prior selection events.

I. General selection functions

II. Node selection functions

III. Edge selection functions

Nodes

clear_selection([type, network, base_url]) If any nodes are selected in the network, they will beunselected.

delete_selected_nodes([network, base_url]) Delete currently selected nodes from the network.get_selected_node_count([network,base_url])

Returns the number of nodes currently selected in thenetwork.

get_selected_nodes([node_suids, network, . . . ]) Retrieve the names of all the nodes selected in the net-work.

invert_node_selection([network, base_url]) Select all nodes that were not selected and deselect allnodes that were selected.

select_all_nodes([network, base_url]) Selects all nodes in a Cytoscape Network.select_first_neighbors([direction, network,. . . ])

Select nodes directly connected to currently selectednodes.

select_nodes(nodes[, by_col, . . . ]) Select nodes in the network by SUID, name or othercolumn values.

select_nodes_connected_by_selected_edges([. . . ])Take currently selected edges and extends the selectionto connected nodes, regardless of directionality.

py4cytoscape.network_selection.clear_selection

clear_selection(type='both', network=None, base_url='http://localhost:1234/v1')If any nodes are selected in the network, they will be unselected.

Parameters

• type (str) – What kinds of objects to deselect: ‘nodes’, ‘edges’ or ‘both’ (default)


5.3. Reference 81



Returns ‘’ empty

Return type str

Raises



Examples

>>> clear_selection()''>>> clear_selection(type='both')''>>> clear_selection(type='nodes', network=52)''

py4cytoscape.network_selection.delete_selected_nodes

delete_selected_nodes(network=None, base_url='http://localhost:1234/v1')Delete currently selected nodes from the network.

Parameters



Returns

{‘nodes’: [node list], ‘edges’: [edge list]} where node list is the SUIDs of deleted nodesand edge list is the SUIDs of deleted edges

Return type dict

Raises







Examples

>>> invert_node_selection(){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}>>> invert_node_selection(network='My Network'){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}>>> invert_node_selection(network=52){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}

py4cytoscape.network_selection.get_selected_node_count

get_selected_node_count(network=None, base_url='http://localhost:1234/v1')Returns the number of nodes currently selected in the network.

Parameters



Returns count of selected nodes

Return type int

Raises



Examples

>>> get_selected_node_count()330>>> get_selected_node_count('My Network')330>>> get_selected_node_count(52)330

py4cytoscape.network_selection.get_selected_nodes

get_selected_nodes(node_suids=False, network=None, base_url='http://localhost:1234/v1')Retrieve the names of all the nodes selected in the network.

Parameters

• node_suids (bool) – Whether to return node SUIDs. Default is FALSE to return nodenames.


5.3. Reference 83




Returns list of selected SUIDs or node names, or None if no nodes are selected

Return type list

Raises



Examples

>>> get_selected_nodes()None>>> get_selected_nodes(node_suids=False)['YNL216W', 'YPL075W']>>> get_selected_nodes(node_suids=True, network='My Network')[10235, 10236]

py4cytoscape.network_selection.invert_node_selection

invert_node_selection(network=None, base_url='http://localhost:1234/v1')Select all nodes that were not selected and deselect all nodes that were selected.

Parameters



Returns {‘nodes’: [node list], ‘edges’: [edge list]}

Return type dict

Raises







Examples

>>> invert_node_selection(){'nodes': [107504, 107503, ...], 'edges': []}>>> invert_node_selection(network='My Network'){'nodes': [107504, 107503, ...], 'edges': []}>>> invert_node_selection(network=52){'nodes': [107504, 107503, ...], 'edges': []}

Note: In return value, node list is the SUIDs of newly selected nodes and edge list is always empty.

py4cytoscape.network_selection.select_all_nodes

select_all_nodes(network=None, base_url='http://localhost:1234/v1')Selects all nodes in a Cytoscape Network.

Parameters

• nodes (list) – List of node SUIDs, names or other column values

• by_col (str) – Node table column to lookup up provide node values. Default is ‘SUID’.

• preserve_current_selection (bool) – Whether to maintain previously selectednodes.



Returns list of SUIDs selected

Return type list

Raises



Examples

>>> select_all_nodes()[107504, 107503, ...]>>> select_all_nodes('My Network')[107504, 107503, ...]>>> select_all_nodes(52)[107504, 107503, ...]

See also:

select_nodes()

5.3. Reference 85



py4cytoscape.network_selection.select_first_neighbors

select_first_neighbors(direction='any', network=None, base_url='http://localhost:1234/v1')Select nodes directly connected to currently selected nodes.

Can specify connection directionality using the direction param.

Parameters

• direction (str) – direction of connections to neighbors to follow, e.g., incoming, out-going, undirected, or any (default)




Return type dict

Raises



Examples

>>> select_first_neighbors(){'nodes': [107504, 107503, ...], 'edges': []}>>> select_first_neighbors(direction='undirected'){'nodes': [107514], 'edges': []}

Note: In the return value, node list is the SUIDs of newly selected nodes and edge list is always empty

py4cytoscape.network_selection.select_nodes

select_nodes(nodes, by_col='SUID', preserve_current_selection=True, network=None,base_url='http://localhost:1234/v1')

Select nodes in the network by SUID, name or other column values.

Parameters

• nodes (list) – List of node SUIDs, names or other column values

• by_col (str) – Node table column to lookup up provide node values. Default is ‘SUID’.

• preserve_current_selection (bool) – Whether to maintain previously selectednodes.







Return type dict

Raises



Examples

>>> select_nodes(None){}>>> select_nodes(['RAP1'], by_col='COMMON'){'nodes': [107514], 'edges': []}

Note: In the return value, node list is the SUIDs of newly selected nodes and edge list is always empty – dict is{} if no nodes were selected

py4cytoscape.network_selection.select_nodes_connected_by_selected_edges

select_nodes_connected_by_selected_edges(network=None, base_url='http://localhost:1234/v1')Take currently selected edges and extends the selection to connected nodes, regardless of directionality.

Parameters




Return type dict

Raises



5.3. Reference 87




Examples

>>> select_nodes_connected_by_selected_edges(){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}>>> select_nodes_connected_by_selected_edges(network='My Network'){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}>>> select_nodes_connected_by_selected_edges(network=52){'nodes': [107504, 107503, ...], 'edges': [108033, 108034]}

Note: In the return value, node list is the SUIDs of selected nodes, and edge list is the SUIDs of newly selectededges

Edges

clear_selection([type, network, base_url]) If any nodes are selected in the network, they will beunselected.

delete_duplicate_edges([network, base_url]) Remove edges with duplicate names.delete_selected_edges([network, base_url]) Delete the currently selected edges in the network.delete_self_loops([network, base_url]) Removes edges that connect to a single node as both

source and target.get_selected_edge_count([network,base_url])

Return the number of edges currently selected in the net-work.

get_selected_edges([edge_suids, network, . . . ]) Retrieve the names of all the edges selected in the net-work.

invert_edge_selection([network, base_url]) Select all edges that were not selected and deselect alledges that were selected.

select_all_edges([network, base_url]) Selects all edges in a Cytoscape Network.select_edges(edges[, by_col, . . . ]) Select edges in the network by SUID, name or other

column values.select_edges_adjacent_to_selected_nodes([. . . ])Take currently selected nodes and add to the selection

all edges connected to those nodes, regardless of direc-tionality.

select_edges_connecting_selected_nodes([. . . ])Select edges in a Cytoscape Network connecting theselected nodes, including self loops connecting singlenodes.

py4cytoscape.network_selection.delete_duplicate_edges

delete_duplicate_edges(network=None, base_url='http://localhost:1234/v1')Remove edges with duplicate names.

Only considers cases with identical source, target, interaction and directionality. Duplicate edges are first se-lected and then deleted. Prior edge selections will be lost; node selections will not be affected.

Parameters


• base_url (str) – Ignore unless you need to specify a custom domain, port or version to



connect to the CyREST API. Default is http://localhost:1234 and the latest version of theCyREST API supported by this version of py4cytoscape.

Returns

{‘nodes’: [node list], ‘edges’: [edge list]} where node list is always empty, and edge list isthe SUIDs of deleted edges – dict is {} if no edges were deleted

Return type dict

Raises



Examples

>>> delete_duplicate_edges(){}>>> delete_duplicate_edges(network='My Network'){'nodes': [], 'edges': [104432, 104431, ...]}>>> delete_duplicate_edges(network=52){'nodes': [], 'edges': [104432, 104431, ...]}

py4cytoscape.network_selection.delete_selected_edges

delete_selected_edges(network=None, base_url='http://localhost:1234/v1')Delete the currently selected edges in the network.

Parameters



Returns

{‘nodes’: [node list], ‘edges’: [edge list]} where node list is always empty, and edge list isthe SUIDs of deleted edges – dict is {} if no edges were deleted

Return type dict

Raises



5.3. Reference 89




Examples

>>> delete_selected_edges(){'nodes': [], 'edges': [104432, 104431, ...]}>>> delete_selected_edges(network='My Network'){}>>> delete_selected_edges(network=52){'nodes': [], 'edges': [104432, 104431, ...]}

py4cytoscape.network_selection.delete_self_loops

delete_self_loops(network=None, base_url='http://localhost:1234/v1')Removes edges that connect to a single node as both source and target.

Self loop edges are first selected and then deleted. Prior edge and node selections will be lost.

Parameters



Returns

’‘

Return type str

Raises



Examples

>>> delete_self_loops()''>>> delete_self_loops(network='My Network')''>>> delete_self_loops(network=52)''




py4cytoscape.network_selection.get_selected_edge_count

get_selected_edge_count(network=None, base_url='http://localhost:1234/v1')Return the number of edges currently selected in the network.

Parameters



Returns count of edges selected in the network

Return type int

Raises



Examples

>>> get_selected_edge_count()0>>> get_selected_edge_count(network='My Network')359>>> get_selected_edge_count(network=52)359

py4cytoscape.network_selection.get_selected_edges

get_selected_edges(edge_suids=False, network=None, base_url='http://localhost:1234/v1')Retrieve the names of all the edges selected in the network.

Parameters

• edge_suids (bool) – Whether to return edge SUIDs. Default is FALSE to return edgenames.



Returns list of edge names (or SUIDs if edge_suids is True) – None if no edges selected

Return type list

Raises


5.3. Reference 91





Examples

>>> get_selected_edges()None>>> get_selected_edge_count(network='My Network')['YGL035C (pd) YIL162W', 'YGL035C (pd) YLR044C', 'YNL216W (pd) YLR044C']>>> get_selected_edge_count(edge_suids=True, network=52)[27656, 27658, 27716]

py4cytoscape.network_selection.invert_edge_selection

invert_edge_selection(network=None, base_url='http://localhost:1234/v1')Select all edges that were not selected and deselect all edges that were selected.

Parameters




Return type dict

Raises



Examples

>>> invert_edge_selection(){'nodes': [], 'edges': [104432, 104431, ...]}>>> invert_edge_selection(network='My Network'){}>>> invert_edge_selection(network=52){'nodes': [], 'edges': [104432, 104431, ...]}

Note: In the return value, node list is always empty, and edge list is the SUIDs of selected edges – dict is {} ifno edges remain selected




py4cytoscape.network_selection.select_all_edges

select_all_edges(network=None, base_url='http://localhost:1234/v1')Selects all edges in a Cytoscape Network.

Parameters



Returns list of SUIDs for edges selected

Return type list

Raises



Examples

>>> select_all_edges()[104432, 104431, ...]>>> select_all_edges(network='My Network')[104432, 104431, ...]>>> select_all_edges(network=52)[104432, 104431, ...]

py4cytoscape.network_selection.select_edges

select_edges(edges, by_col='SUID', preserve_current_selection=True, network=None,base_url='http://localhost:1234/v1')

Select edges in the network by SUID, name or other column values.

Parameters

• edges (list) – List of edge SUIDs, names or other column values

• by.col (str) – Edge table column to lookup up provide edge values. Default is ‘SUID’.

• preserve_current_selection (bool) – Whether to maintain previously selectededges.




Return type dict

5.3. Reference 93




Raises



Examples

>>> select_edges(None){}>>> select_edges([103332], preserve_current_selection=False, network='My Network'){'nodes': [], 'edges': [108033, 108034]}>>> select_edges(['YGL035C (pd) YIL162W', 'YGL035C (pd) YLR044C', 'YNL216W (pd)→˓YLR044C'], by_col='name', preserve_current_selection=True, network=52){'nodes': [], 'edges': [108033, 108034, 108103]}

Note: In the return value, node list is always empty, and edge list is the SUIDs of newly selected edges – dictis {} if no edges were selected

py4cytoscape.network_selection.select_edges_adjacent_to_selected_nodes

select_edges_adjacent_to_selected_nodes(network=None, base_url='http://localhost:1234/v1')Take currently selected nodes and add to the selection all edges connected to those nodes, regardless of direc-tionality.

Any edges selected beforehand are deselected before any new edges are selected

Parameters




Return type dict

Raises






Examples

>>> select_edges_adjacent_to_selected_nodes(){}>>> select_edges_adjacent_to_selected_nodes(network='My Network'){'nodes': [103990, 103991, ...], 'edges': [104432, 104431, ...]}>>> select_edges_adjacent_to_selected_nodes(network=52){'nodes': [103990, 103991, ...], 'edges': [104432, 104431, ...]}

Note: In the return value, node list is list of all selected edges, and edge list is the SUIDs of selected edges –dict is {} if no nodes were selected or there were no newly created edges

py4cytoscape.network_selection.select_edges_connecting_selected_nodes

select_edges_connecting_selected_nodes(network=None, base_url='http://localhost:1234/v1')Select edges in a Cytoscape Network connecting the selected nodes, including self loops connecting singlenodes.

Any edges selected beforehand are deselected before any new edges are selected

Parameters




Return type dict

Raises



Examples

>>> select_edges_connecting_selected_nodes()None>>> select_edges_connecting_selected_nodes(network='My Network'){'nodes': [103990, 103991, ...], 'edges': [104432, 104431, ...]}>>> select_edges_connecting_selected_nodes(network=52){'nodes': [103990, 103991, ...], 'edges': [104432, 104431, ...]}

Note: In the return value node list is list of all selected nodes, and edge list is the SUIDs of selected edges –dict is None if no nodes were selected or there were no newly created edges

5.3. Reference 95



Network Views

Functions for performing VIEW operations in addition to getting and setting view properties.

Views

export_image([filename, type, resolution, . . . ]) Save the current network view as an image file.fit_content([selected_only, network, base_url]) Zoom and pan network view to maximize either height

or width of current network window.get_network_view_suid([network, base_url]) Retrieve the SUID of a network view.get_network_views([network, base_url]) Retrieve list of network view SUIDs.set_current_view([network, base_url]) Set which network view is “current”.toggle_graphics_details([base_url]) Toggle Graphics Details.

py4cytoscape.network_views.export_image

export_image(filename=None, type='PNG', resolution=None, units=None, height=None, width=None,zoom=None, network=None, base_url='http://localhost:1234/v1')

Save the current network view as an image file.

The image is cropped per the current view in Cytoscape. Consider applying fit_content() prior to export.

Parameters

• filename (str) – Full path or path relavtive to current working directory, in addition tothe name of the file. Extension is automatically added based on the type argument. Ifblank, the current network name will be used.

• type (str) – Type of image to export, e.g., PNG (default), JPEG, PDF, SVG, PS(PostScript).

• resolution (int) – The resolution of the exported image, in DPI. Valid only for bitmapformats, when the selected width and height ‘units’ is inches. The possible values are: 72(default), 100, 150, 300, 600.

• units (str) – The possible values are: pixels (default), inches.

• height (float) – The height of the exported image. Valid only for bitmap formats, suchas PNG and JPEG.

• width (float) – The width of the exported image. Valid only for bitmap formats, suchas PNG and JPEG.

• zoom (float) – The zoom value to proportionally scale the image. The default value is100.0. Valid only for bitmap formats, such as PNG and JPEG

• network (str or SUID or None) – Name or SUID of the network or view. Defaultis the “current” network active in Cytoscape. If a network view SUID is provided, then it isvalidated and returned.


Returns {‘file’: name of file} contains absolute path to file that was written

Return type dict




Raises

• CyError – if network or view doesn’t exist


Examples

>>> export_image('output/test', type='JPEG', units='pixels', height=1000,→˓width=2000, zoom=200){"file": "C:\Users\CyDeveloper\tests\output\test.jpeg">>> export_image('output/test', type='PDF', network='My Network'){"file": "C:\Users\CyDeveloper\tests\output\test.pdf">>> export_image(type='PNG', resolution=600, units='inches', height=1.7, width=3.→˓5, zoom=500, network=13098){"file": "C:\Users\CyDeveloper\tests\output\test.png"

py4cytoscape.network_views.fit_content

fit_content(selected_only=False, network=None, base_url='http://localhost:1234/v1')Zoom and pan network view to maximize either height or width of current network window.

Takes first (presumably only) view associated with provided network

Parameters

• selected_only (bool) – Whether to fit only current selection. Default is false, i.e., tofit the entire network



Returns {}

Return type dict

Raises



5.3. Reference 97



Examples

>>> fit_content(){}>>> fit_content(51, selected_only=True){}>>> fit_content(network='galFiltered.sif'){}

py4cytoscape.network_views.get_network_view_suid

get_network_view_suid(network=None, base_url='http://localhost:1234/v1')Retrieve the SUID of a network view.

Parameters



Returns SUID of the view for the network. The first (presummably only) view associated a networkis returned.

Return type int

Raises



Examples

>>> get_network_view_suid()130223>>> get_network_view_suid(51)130223>>> get_network_view_suid(network='galFiltered.sif')130223

Dev Notes: analogous to getNetworkSuid, this function attempts to handle all of the multiple ways we sup-port network view referencing (e.g., title, SUID, ‘current’, and NULL). These functions are then used byfunctions that take a “network” argument and requires a view SUID.




py4cytoscape.network_views.get_network_views

get_network_views(network=None, base_url='http://localhost:1234/v1')Retrieve list of network view SUIDs.

Parameters

• network (str or SUID or None) – Name or SUID of the network. Default is the“current” network active in Cytoscape.


Returns [list of SUIDs of views] where the list has length 1

Return type list

Raises

• CyError – if network doesn’t exist


Examples

>>> get_network_views()[130223]>>> get_network_views(51)[130223]>>> get_network_views(network='galFiltered.sif')[130223]

py4cytoscape.network_views.set_current_view

set_current_view(network=None, base_url='http://localhost:1234/v1')Set which network view is “current”.

Takes first (presumably only) view associated with provided network

Parameters



Returns {}

Return type dict

Raises


5.3. Reference 99





Examples

>>> set_current_view(){}>>> set_current_view(51){}>>> set_current_view(network='galFiltered.sif'){}

py4cytoscape.network_views.toggle_graphics_details

toggle_graphics_details(base_url='http://localhost:1234/v1')Toggle Graphics Details.

Regardless of the current zoom level and network size, show (or hide) graphics details, e.g., node labels.

Displaying graphics details on a very large network will affect pan and zoom performance, depending on youravailable RAM. See cytoscape_memory_status().

Parameters



Returns {‘message’: ‘Toggled Graphics level of details.’}

Return type dict

Raises



Examples

>>> toggle_graphics_details(){'message': 'Toggled Graphics level of details.'}




5.3.11 Session

Functions for managing Cytoscape SESSIONS, including save, open and close.

Session

close_session(save_before_closing[, . . . ]) Close the current session in Cytoscape, destroying allunsaved work.

open_session([file_location, base_url]) Open Session File or URL.save_session([filename, base_url]) Saves the current Cytoscape session as a CYS file.

py4cytoscape.session.close_session

close_session(save_before_closing, filename=None, base_url='http://localhost:1234/v1')Close the current session in Cytoscape, destroying all unsaved work.

A boolean for whether to save before closing is required since you could lose data by closing without saving.

Parameters

• save_before_closing (bool) – Whether to save before closing the current session.If False, then all unsaved work will be lost.

• filename (str) – If save_before_closing is True and the session has not previ-ously been saved, then the path and name of the session file to save should be provided.


Returns {} empty

Return type dict

Raises

• CyError – if filename is invalid


Examples

>>> close_session(False) # delete the current session without saving it first{}>>> close_session(True) # delete the current session after saving it to the file→˓it came from{}>>> close_session(True, 'new') # delete the current session after saving it to→˓'new.cys'{}

5.3. Reference 101



py4cytoscape.session.open_session

open_session(file_location=None, base_url='http://localhost:1234/v1')Open Session File or URL.

Open a session file or URL. This will clear all networks, tables and styles associated with current session. Besure to saveSession first.

Parameters

• file_location (str) – File path or URL (with ‘http’ or ‘https’ prefix). Default is asample session file.


Returns {} empty

Return type dict

Raises



Examples

>>> open_session() # load session from sample Yeast Perturbation.cys file{}>>> open_session('data/Affinity Purification.cys') # load session from a file{}>>> open_session('https://github.com/bdemchak/py4cytoscape/blob/master/tests/data/→˓Affinity%20Purification.cys'){}

See also:

save_session()

py4cytoscape.session.save_session

save_session(filename=None, base_url='http://localhost:1234/v1')Saves the current Cytoscape session as a CYS file.

If no filename is provided, then it attempts to save to an existing CYS file associated with the session. Iffilename already exists, then it is overwritten.

Parameters

• filename (str) – Full path or path relavtive to current working directory, in addition tothe name of the file. The .cys extension is automatically added. Leave blank to updatepreviously saved session file.






Returns {} empty

Return type dict

Raises



Examples

>>> save_session('other') # Save current session as other.cys{}>>> save_session('other.cys') # Save current session as other.cys{}>>> save_session() # Save current session back to the same file it was loaded from{}

5.3.12 Styles

Basic Styles

Functions for managing STYLES and retrieving general lists of properties relevant to multiple style modes. Functionsspecific to Default, Mapping, Bypass, Dependencies and Values are in separate files.

I. Style management functions

II. General property functions

Style Management

copy_visual_style(from_style, to_style[, . . . ]) Create a new visual style by copying a specified style.create_visual_style(style_name[, defaults,. . . ])

Create a style from defaults and predefined mappings.

delete_visual_style(style_name[, base_url]) Delete the specified visual style from current session.export_visual_styles([filename, type, . . . ]) Save one or more visual styles to file.get_visual_style_names([base_url]) Retrieve a list of all visual style names.import_visual_styles([filename, base_url]) Load styles from an XML file and returns the names of

the loaded styles.set_visual_style(style_name[, network,base_url])

Apply a visual style to a network.

5.3. Reference 103


py4cytoscape.styles.copy_visual_style

copy_visual_style(from_style, to_style, base_url='http://localhost:1234/v1')Create a new visual style by copying a specified style.

Parameters

• from_style (str) – Name of visual style to copy

• to_style (str) – Name of new visual style


Returns

’‘

Return type str

Raises

• CyError – if style doesn’t exist


Examples

>>> copy_visual_style('Solid', 'SolidCopy')''

py4cytoscape.styles.create_visual_style

create_visual_style(style_name, defaults=None, mappings=None,base_url='http://localhost:1234/v1')

Create a style from defaults and predefined mappings.

Requires visual property mappings to be previously created, see map_visual_property.

Parameters

• style_name (str) – name for style

• defaults (list) – key-value pairs for default mappings.

• mappings (list) – visual property mappings, see map_visual_property


Returns {‘title’: new style name}

Return type dict

Raises

• CyError – if mappings or defaults contain invalid values






Examples

>>> defaults = {'NODE_SHAPE': 'diamond', 'NODE_SIZE': 30, 'EDGE_TRANSPARENCY':→˓120, 'NODE_LABEL_POSITION': 'W,E,c,0.00,0.00'}>>> node_labels = map_visual_property('node label', 'COMMON', 'p')>>> node_fills = map_visual_property('node fill color', 'Degree', 'd', ['1', '2'],→˓ ['#FF9900', '#66AAAA'])>>> arrow_shapes = map_visual_property('Edge Target Arrow Shape', 'interaction',→˓'d', ['pp', 'pd'], ['Arrow', 'T'])>>> edge_width = map_visual_property('edge width', 'EdgeBetweenness', 'p')>>> create_visual_style('NewStyle', defaults=defaults, mappings=[node_labels,→˓node_fills, arrow_shapes, edge_width]){'title': 'NewStyle'}

Note: To apply the style to a network, first create the network and then call set_visual_style

See also:

map_visual_property(), set_visual_style()

py4cytoscape.styles.delete_visual_style

delete_visual_style(style_name, base_url='http://localhost:1234/v1')Delete the specified visual style from current session.

Parameters

• style_name (str) – name of style to delete


Returns

’‘

Return type str

Raises

• CyError – if the style doesn’t exist


5.3. Reference 105



Examples

>>> delete_visual_style('NewStyle')''

py4cytoscape.styles.export_visual_styles

export_visual_styles(filename=None, type='XML', styles=None, base_url='http://localhost:1234/v1')Save one or more visual styles to file.

Parameters

• filename (str) – Full path or path relavtive to current working directory, in addition tothe name of the file. Extension is automatically added based on the type argument. Defaultis “styles.xml”

• type (str) – Type of data file to export, e.g., XML, JSON (case sensitive). Default isXML. Note: Only XML can be read by import_visual_styles().

• styles (str) – specified, only the current one is exported.


Returns {‘file’: name of file written}

Return type dict

Raises

• CyError – if the output file can’t be created


Examples

>>> export_visual_styles() # export the current style to styles.xml in the→˓current directory{'file': 'C:\Users\CyDeveloper\styles.xml'}>>> export_visual_styles('curstyle') # export the current style to curstyle.xml→˓in the current directory{'file': 'C:\Users\CyDeveloper\curstyle.xml'}>>> export_visual_styles('curstyle', type='json') # export the current style in→˓cytoscape.js format{'file': 'C:\Users\CyDeveloper\curstyle.json'}

See also:

import_visual_styles()




py4cytoscape.styles.get_visual_style_names

get_visual_style_names(base_url='http://localhost:1234/v1')Retrieve a list of all visual style names.


Returns [names of styles in session]

Return type list


Examples

>>> visual_style_names()['Universe', 'Marquee', 'Big Labels', 'BioPAX_SIF', 'Ripple', 'Metallic',→˓'default black', ...]

py4cytoscape.styles.import_visual_styles

import_visual_styles(filename='styles.xml', base_url='http://localhost:1234/v1')Load styles from an XML file and returns the names of the loaded styles.

Parameters

• filename (str) – Name of the style file to load. Only reads XML files. Default is“styles.xml”.


Returns [names of styles loaded]

Return type list

Raises

• CyError – if the input file can’t be read


5.3. Reference 107




Examples

>>> import_visual_styles() # export styles.xml in the current directory['galFiltered Style']>>> import_visual_styles('curstyle.xml') # export curstyle.xml in the current→˓directory['galFiltered Style']

See also:

export_visual_styles()

py4cytoscape.styles.set_visual_style

set_visual_style(style_name, network=None, base_url='http://localhost:1234/v1')Apply a visual style to a network.

Parameters

• style_name (str) – Name of a visual style


Returns {‘message’: ‘Visual Style applied.’}

Return type dict

Raises

• CyError – if style doesn’t exist or network doesn’t exist


Examples

>>> set_visual_style('default'){'message': 'Visual Style applied.'}>>> set_visual_style('galFiltered Style', network=51){'message': 'Visual Style applied.'}

Visual Property Names and Values

get_arrow_shapes([base_url]) Get Arrow Shapes.get_line_styles([base_url]) Get Line Styles.get_node_shapes([base_url]) Get Node Shapes.get_visual_property_names([base_url]) Retrieve the names of all possible visual properties.




py4cytoscape.styles.get_arrow_shapes

get_arrow_shapes(base_url='http://localhost:1234/v1')Get Arrow Shapes.

Retrieve the names of the currently supported ‘arrows’ – the decorations can (optionally) appear at the ends ofedges, adjacent to the nodes they connect, and conveying information about the nature of the nodes’ relationship.


Returns [arrow shape names]

Return type list


Examples

>>> get_arrow_shapes()['OPEN_CIRCLE', 'SQUARE', 'CIRCLE', 'DELTA_SHORT_2', 'DELTA', 'DIAMOND_SHORT_2', .→˓..]

py4cytoscape.styles.get_line_styles

get_line_styles(base_url='http://localhost:1234/v1')Get Line Styles.

Retrieve the names of the currently supported line types – values which can be used to render edges, and thuscan be used in calls to set_edge_line_style_rule().


Returns [line style names]

Return type list


Examples

>>> get_line_styles()['MARQUEE_DASH_DOT', 'SOLID', 'BACKWARD_SLASH', 'EQUAL_DASH', 'CONTIGUOUS_ARROW',→˓...]

5.3. Reference 109




py4cytoscape.styles.get_node_shapes

get_node_shapes(base_url='http://localhost:1234/v1')Get Node Shapes.

Retrieve the names of the currently supported node shapes, which can then be used in calls toset_node_shape_rule() and set_default_viz_map_value().


Returns [node shape names]

Return type list


Examples

>>> get_node_shapes()['ROUND_RECTANGLE', 'VEE', 'TRIANGLE', 'HEXAGON', 'PARALLELOGRAM', 'ELLIPSE',→˓'OCTAGON', ...]

py4cytoscape.styles.get_visual_property_names

get_visual_property_names(base_url='http://localhost:1234/v1')Retrieve the names of all possible visual properties.


Returns [visual property names]

Return type list


Examples

>>> get_visual_property_names()['COMPOUND_NODE_PADDING', 'COMPOUND_NODE_SHAPE', 'DING_RENDERING_ENGINE_ROOT',→˓'EDGE', ...]





Style Bypasses

Functions for getting and setting BYPASS values for visual properties, organized into sections:

I. General functions for setting/clearing node, edge and network properties

II. Specific functions for setting particular node, edge and network properties

NOTE: The CyREST ‘bypass’ endpoint is essential to properly set values that will persist for a given network inde-pendent of applied style and style changes, and from session to session if saved.

General Style Bypasses

set_node_property_bypass(node_names, . . . [,. . . ])

Set Node Property Bypass.

set_edge_property_bypass(edge_names, . . . [,. . . ])

Set Edge Property Bypass.

py4cytoscape.style_bypasses.set_node_property_bypass

set_node_property_bypass(node_names, new_values, visual_property, bypass=True, network=None,base_url='http://localhost:1234/v1')

Set Node Property Bypass.

Set bypass values for any node property of the specified nodes, overriding default values and mappings definedby any visual style.

This method permanently overrides any default values or mappings defined for the visual properties of the nodeor nodes specified. To restore defaults and mappings, use clear_node_property_bypass().

Parameters

• node_names (list) – List of node names

• new_values (list) – List of values to set, or single value

• visual_property (str) – Name of a visual property. Seeget_visual_property_names.

• bypass (bool) – Whether to set permanent bypass value. Default is True



Returns

’‘

Return type str

Raises

• CyError – if node, visual property or network name doesn’t exist


5.3. Reference 111



Examples

>>> node_names = list(get_table_columns(columns='name')['name'])>>> set_node_property_bypass(node_names, '#FF00FF', 'NODE_FILL_COLOR')>>> ''>>> node_suids = list(get_table_columns(columns='name').index)>>> set_node_property_bypass(node_suids, ['#FF00FF'], 'NODE_FILL_COLOR', network=→˓'galFiltered.sif')>>> ''

See also:

clear_node_property_bypass()

py4cytoscape.style_bypasses.set_edge_property_bypass

set_edge_property_bypass(edge_names, new_values, visual_property, bypass=True, network=None,base_url='http://localhost:1234/v1')

Set Edge Property Bypass.

Set bypass values for any edge property of the specified edges, overriding default values and mappings definedby any visual style.

This method permanently overrides any default values or mappings defined for the visual properties of the edgeor edges specified. To restore defaults and mappings, use clear_edge_property_bypass().

Parameters

• edge_names (list) – List of edgenames

• new_values (list) – List of values to set, or single value





Returns

’‘

Return type str

Raises

• CyError – if edge, visual property or network name doesn’t exist





Examples

>>> edge_names = list(get_table_columns(table='edge', columns='name')['name'])>>> set_edge_property_bypass(edge_names, '#FF00FF', 'EDGE_UNSELECTED_PAINT')>>> {'data': {}, 'errors': []}>>> edge_suids = list(get_table_columns(table='edge', columns='name').index)>>> set_edge_property_bypass(edge_suids, ['#FF00FF'], 'EDGE_UNSELECTED_PAINT',→˓network='galFiltered.sif')>>> {'data': {}, 'errors': []}

See also:

clear_edge_property_bypass()

Node Style Bypasses

clear_node_opacity_bypass(node_names[,. . . ])

Clear Node Opacity Bypass.

clear_node_property_bypass(node_names,. . . )

Clear Node Property Bypass.

hide_nodes(node_names[, network, base_url]) Hide Nodes.hide_selected_nodes([network, base_url]) Hide Selected Nodes.set_node_border_color_bypass(node_names,. . . )

Override the border color for particular nodes.

set_node_border_opacity_bypass(node_names,. . . )

Override the border opacity for particular nodes.

set_node_border_width_bypass(node_names,. . . )

Override the border width for particular nodes.

set_node_color_bypass(node_names,new_colors)

Set the bypass value for fill color for the specified nodeor nodes.

set_node_fill_opacity_bypass(node_names,. . . )

Override the fill opacity for particular nodes.

set_node_font_face_bypass(node_names,new_fonts)

Override the font face for particular nodes.

set_node_font_size_bypass(node_names,new_sizes)

Override the font size for particular nodes.

set_node_height_bypass(node_names,new_heights)

Override the height for particular nodes.

set_node_label_bypass(node_names,new_labels)

Override the label for particular nodes.

set_node_label_color_bypass(node_names,. . . )

Override the label color for particular nodes.

set_node_label_opacity_bypass(node_names,. . . )

Override the label opacity for particular nodes.

set_node_opacity_bypass(node_names,new_values)

Set the bypass value for node fill, label and border opac-ity for the specified node or nodes.

set_node_shape_bypass(node_names,new_shapes)

Override the shape for particular nodes

set_node_size_bypass(node_names, new_sizes) Set Node Size Bypass.set_node_tooltip_bypass(node_names,new_tooltip)

Sets a bypass tooltip for one or more nodes.

continues on next page

5.3. Reference 113


Table 30 – continued from previous pageset_node_width_bypass(node_names,new_widths)

Override the width for particular nodes.

unhide_nodes(node_names[, network, base_url]) Unhide Nodes.

py4cytoscape.style_bypasses.clear_node_opacity_bypass

clear_node_opacity_bypass(node_names, network=None, base_url='http://localhost:1234/v1')Clear Node Opacity Bypass.

Clear the bypass value for node fill, label and border opacity for the specified node or nodes, effectively restoringany previously defined style defaults or mappings.

Parameters

• node_names (list) – list of node names



Returns {‘data’: {}, ‘errors’: []}

Return type dict

Raises

• CyError – if node or network name doesn’t exist


Examples

>>> clear_node_opacity_bypass(get_node_names())>>> ''>>> clear_node_opacity_bypass(['YDL194W', 'YBR043C'], network='galFiltered.sif')>>> ''

See also:

set_node_opacity_bypass()

py4cytoscape.style_bypasses.clear_node_property_bypass

clear_node_property_bypass(node_names, visual_property, network=None,base_url='http://localhost:1234/v1')

Clear Node Property Bypass.

Clear bypass values for any node property of the specified nodes, effectively restoring any previously definedstyle defaults or mappings.

Parameters

• node_names (list) – List of node names









Return type dict

Raises


• TypeError – if node list is None


Examples

>>> node_names = list(get_table_columns(columns='name')['name'])>>> clear_node_property_bypass(node_names, 'NODE_FILL_COLOR')>>> ''>>> node_suids = list(get_table_columns(columns='name').index)>>> clear_node_property_bypass(node_suids, 'NODE_FILL_COLOR', network=→˓'galFiltered.sif')>>> ''

See also:

set_node_property_bypass()

py4cytoscape.style_bypasses.hide_nodes

hide_nodes(node_names, network=None, base_url='http://localhost:1234/v1')Hide Nodes.

Hide (but do not delete) the specified node or nodes, by setting the Visible property bypass value to false.

This method permanently overrides any default values or mappings defined for this visual property of the nodeor nodes specified. This method ultimately calls the generic function, set_node_property_bypass(),which can be used to set any visual property. To restore defaults and mappings, use unhide_nodes() orunhide_all().

Parameters




5.3. Reference 115




Returns

’‘

Return type str

Raises



Examples

>>> hide_nodes(get_node_names())>>> ''>>> hide_nodes(['YDL194W', 'YBR043C'], network='galFiltered.sif')>>> ''

See also:

set_node_property_bypass(), hide_nodes(), unhide_nodes(), unhide_all()

py4cytoscape.style_bypasses.hide_selected_nodes

hide_selected_nodes(network=None, base_url='http://localhost:1234/v1')Hide Selected Nodes.

Hide (but do not delete) the currently selected nodes, by setting the Visible property bypass value to false.

This method permanently overrides any default values or mappings defined for this visual property of the nodeor nodes specified. This method ultimately calls the generic function, set_node_property_bypass(),which can be used to set any visual property. To restore defaults and mappings, use unhide_nodes() orunhide_all().

Parameters



Returns

’‘

Return type str

Raises

• CyError – if network name doesn’t exist





Examples

>>> hide_selected_nodes()>>> ''>>> hide_selected_nodes(network='galFiltered.sif')>>> ''

See also:

set_node_property_bypass(), hide_nodes(), unhide_nodes(), unhide_all()

py4cytoscape.style_bypasses.set_node_border_color_bypass

set_node_border_color_bypass(node_names, new_colors, network=None,base_url='http://localhost:1234/v1')

Override the border color for particular nodes.

This method permanently overrides any default values or mappings defined for this visualproperty of the node or nodes specified. This method ultimately calls the generic function,set_node_property_bypass() which can be used to set any visual property. To restore defaultsand mappings, use clear_node_property_bypass(), see examples.

Parameters


• new_colors (str or list) – list of hex colors or single value



Returns ‘’ (None if invalid color is found in new_colors)

Return type str

Raises



Examples

>>> set_node_border_color_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_border_color_bypass(['YDL194W', 'YBR043C'], ['#FF00FF', '#CCCCCC'],→˓network='galFiltered.sif')>>> ''

See also:

set_node_property_bypass(), clear_node_property_bypass()

5.3. Reference 117



py4cytoscape.style_bypasses.set_node_border_opacity_bypass

set_node_border_opacity_bypass(node_names, new_values, network=None,base_url='http://localhost:1234/v1')

Override the border opacity for particular nodes.


Parameters


• new_values (int or float or list) – list of values to set, or single value



Returns ‘’ (None if invalid opacity is found in new_values)

Return type str

Raises



Examples

>>> set_node_border_opacity_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_border_opacity_bypass(['YDL194W', 'YBR043C'], [128, 192], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_border_width_bypass

set_node_border_width_bypass(node_names, new_sizes, network=None,base_url='http://localhost:1234/v1')

Override the border width for particular nodes.


Parameters





• new_sizes (int or float or list) – list of size values or single value



Returns ‘’ (None if size is invalid)

Return type str

Raises



Examples

>>> set_node_border_width_bypass(get_node_names(), 10)>>> ''>>> set_node_border_width_bypass(['YDL194W', 'YBR043C'], [10, 20.5], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_color_bypass

set_node_color_bypass(node_names, new_colors, network=None,base_url='http://localhost:1234/v1')

Set the bypass value for fill color for the specified node or nodes.


Parameters






Return type str

5.3. Reference 119




Raises



Examples

>>> set_node_color_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_color_bypass(['YDL194W', 'YBR043C'], ['#FF00FF', '#CCCCCC'], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_fill_opacity_bypass

set_node_fill_opacity_bypass(node_names, new_values, network=None,base_url='http://localhost:1234/v1')

Override the fill opacity for particular nodes.


Parameters






Return type str

Raises






Examples

>>> set_node_fill_opacity_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_fill_opacity_bypass(['YDL194W', 'YBR043C'], [128, 192], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_font_face_bypass

set_node_font_face_bypass(node_names, new_fonts, network=None,base_url='http://localhost:1234/v1')

Override the font face for particular nodes.


Parameters


• new_fonts (str or list) – list of font values or single value



Returns

’‘

Return type str

Raises



Examples

>>> set_node_font_face_bypass(get_node_names(), 'Dialog.italic,plain,20')>>> ''>>> set_node_font_face_bypass(['YDL194W', 'YBR043C'], ['Dialog.italic,plain,20',→˓'Dialog.bold,plain,10'], network='galFiltered.sif')>>> ''

See also:


5.3. Reference 121



py4cytoscape.style_bypasses.set_node_font_size_bypass

set_node_font_size_bypass(node_names, new_sizes, network=None,base_url='http://localhost:1234/v1')

Override the font size for particular nodes.


Parameters


• new_sizes (int or float or list) – list of font sizes or single value



Returns

’‘

Return type str

Raises



Examples

>>> set_node_font_size_bypass(get_node_names(), 20)>>> ''>>> set_node_font_size_bypass(['YDL194W', 'YBR043C'], [50, 100], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_height_bypass

set_node_height_bypass(node_names, new_heights, network=None,base_url='http://localhost:1234/v1')

Override the height for particular nodes.





Parameters


• new_heights (int or float or list) – list of height values or single value



Returns ‘’ (None if height is invalid)

Return type str

Raises



Examples

>>> set_node_height_bypass(get_node_names(), 80)>>> ''>>> set_node_height_bypass(['YDL194W', 'YBR043C'], [80, 100.5], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_label_bypass

set_node_label_bypass(node_names, new_labels, network=None,base_url='http://localhost:1234/v1')

Override the label for particular nodes.


Parameters


• new_labels (str or list) – list of label values or single value



5.3. Reference 123




Returns

’‘

Return type str

Raises



Examples

>>> set_node_label_bypass(get_node_names(), 'test label')>>> ''>>> set_node_label_bypass(['YDL194W', 'YBR043C'], ['A', 'B'], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_label_color_bypass

set_node_label_color_bypass(node_names, new_colors, network=None,base_url='http://localhost:1234/v1')

Override the label color for particular nodes.


Parameters


• new_colors (str or list) – list of hex colors, or single value



Returns ‘’ (None if invalid color)

Return type str

Raises






Examples

>>> set_node_label_color_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_label_color_bypass(['YDL194W', 'YBR043C'], ['#FF00FF', '#FFFF00'],→˓network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_label_opacity_bypass

set_node_label_opacity_bypass(node_names, new_values, network=None,base_url='http://localhost:1234/v1')

Override the label opacity for particular nodes.


Parameters






Return type str

Raises



Examples

>>> set_node_label_opacity_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_label_opacity_bypass(['YDL194W', 'YBR043C'], [128, 192], network=→˓'galFiltered.sif')>>> ''

See also:


5.3. Reference 125



py4cytoscape.style_bypasses.set_node_opacity_bypass

set_node_opacity_bypass(node_names, new_values, network=None,base_url='http://localhost:1234/v1')

Set the bypass value for node fill, label and border opacity for the specified node or nodes.


Parameters






Return type str

Raises



Examples

>>> set_node_opacity_bypass(get_node_names(), '#FF00FF')>>> ''>>> set_node_opacity_bypass(['YDL194W', 'YBR043C'], [128, 192], network=→˓'galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_shape_bypass

set_node_shape_bypass(node_names, new_shapes, network=None,base_url='http://localhost:1234/v1')

Override the shape for particular nodes


Parameters





• new_shapes (str or list) – List of shapes, or single value. Seeget_node_shapes().



Returns ‘’ (None if invalid shape)

Return type str

Raises



Examples

>>> set_node_shape_bypass(get_node_names(), 'ROUND_RECTANGLE')>>> ''>>> set_node_shape_bypass(['YDL194W', 'YBR043C'], ['ROUND_RECTANGLE', 'OCTAGON'],→˓network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_size_bypass

set_node_size_bypass(node_names, new_sizes, network=None, base_url='http://localhost:1234/v1')Set Node Size Bypass.


Parameters


• new_sizes (int or float or list) – list of size values or single value



Returns ‘’ (None if invalid size is found in new_sizes)

Return type str

5.3. Reference 127




Raises



Examples

>>> set_node_size_bypass(get_node_names(), 50)>>> ''>>> set_node_size_bypass(['YDL194W', 'YBR043C'], [150.5, 90.5], network=→˓'galFiltered.sif')>>> ''

Note: Sets the bypass value of node size for one or more nodes. Only applicable if node dimensions are locked.See lockNodeDimensions().

See also:


py4cytoscape.style_bypasses.set_node_tooltip_bypass

set_node_tooltip_bypass(node_names, new_tooltip, network=None,base_url='http://localhost:1234/v1')

Sets a bypass tooltip for one or more nodes.


Parameters


• new_tooltip (str or list) – list of size values or single value



Returns

’‘

Return type str

Raises






Examples

>>> set_node_tooltip_bypass(get_node_names(), 'Some Tooltip')>>> ''>>> set_node_tooltip_bypass(['YDL194W', 'YBR043C'], ['One Tooltip', 'Other Tooltip→˓'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_node_width_bypass

set_node_width_bypass(node_names, new_widths, network=None,base_url='http://localhost:1234/v1')

Override the width for particular nodes.


Parameters


• new_widths (int or float or list) – list of width values or single value



Returns ‘’ (None if width is invalid)

Return type str

Raises



Examples

>>> set_node_width_bypass(get_node_names(), 80)>>> ''>>> set_node_width_bypass(['YDL194W', 'YBR043C'], [80, 100.5], network=→˓'galFiltered.sif')>>> ''

See also:


5.3. Reference 129



py4cytoscape.style_bypasses.unhide_nodes

unhide_nodes(node_names, network=None, base_url='http://localhost:1234/v1')Unhide Nodes.

Unhide specified nodes that were previously hidden, by clearing the Node Visible property bypass value.

This method ultimately calls the generic function, clear_node_property_bypass(), which can be usedto clear any visual property.

Parameters





Return type dict

Raises



Examples

>>> hide_nodes(get_node_names())>>> ''>>> hide_nodes(['YDL194W', 'YBR043C'], network='galFiltered.sif')>>> ''

See also:

clear_node_property_bypass(), unhide_all()

Edge Style Bypasses

clear_edge_property_bypass(edge_names,. . . )

Clear Edge Property Bypass.

hide_edges(edge_names[, network, base_url]) Hide Edges.hide_selected_edges([network, base_url]) Hide Selected Edges.set_edge_color_bypass(edge_names,new_colors)

Set the bypass value for fill color for the specified edgeor edges.

set_edge_font_face_bypass(edge_names,new_fonts)

Override the font face for particular edges.

set_edge_font_size_bypass(edge_names,new_sizes)

Override the font size for particular edges.





Table 31 – continued from previous pageset_edge_label_bypass(edge_names,new_labels)

Override the label for particular edges.

set_edge_label_color_bypass(edge_names,. . . )

Override the label color for particular edges.

set_edge_label_opacity_bypass(edge_names,. . . )

Override the label opacity for particular edges.

set_edge_line_style_bypass(edge_names,. . . )

Override the style for particular edges.

set_edge_line_width_bypass(edge_names,. . . )

Override the width for particular edges.

set_edge_opacity_bypass(edge_names,new_values)

Override the opacity for particular edges.

set_edge_source_arrow_color_bypass(. . . [,. . . ])

Override the target arrow color for particular edges.

set_edge_source_arrow_shape_bypass(. . . [,. . . ])

Override the source arrow shape for particular edges.

set_edge_target_arrow_color_bypass(. . . [,. . . ])


set_edge_target_arrow_shape_bypass(. . . [,. . . ])

Override the target arrow shape for particular edges.

set_edge_tooltip_bypass(edge_names,new_tooltip)

Sets a bypass tooltip for one or more edges.

unhide_edges(edge_names[, network, base_url]) Unhide Edges.

py4cytoscape.style_bypasses.clear_edge_property_bypass

clear_edge_property_bypass(edge_names, visual_property, network=None,base_url='http://localhost:1234/v1')

Clear Edge Property Bypass.

Clear bypass values for any edge property of the specified edges, effectively restoring any previously definedstyle defaults or mappings.

Parameters

• edge_names (list) – List of edge names






Return type dict

Raises


5.3. Reference 131



• TypeError – if node list is None


Examples

>>> edge_names = list(get_table_columns(table='edge', columns='name')['name'])>>> clear_edge_property_bypass(edge_names, 'EDGE_UNSELECTED_PAINT')>>> {'data': {}, 'errors': []}>>> edge_suids = list(get_table_columns(table='edge', columns='name').index)>>> clear_edge_property_bypass(edge_suids, 'EDGE_UNSELECTED_PAINT', network=→˓'galFiltered.sif')>>> {'data': {}, 'errors': []}

See also:

set_edge_property_bypass()

py4cytoscape.style_bypasses.hide_edges

hide_edges(edge_names, network=None, base_url='http://localhost:1234/v1')Hide Edges.

Hide (but do not delete) the specified edge or edges, by setting the Visible property bypass value to false.

This method permanently overrides any default values or mappings defined for this visual property of the edgeor edges specified. This method ultimately calls the generic function, set_edge_property_bypass(),which can be used to set any visual property. To restore defaults and mappings, use unhide_edges() orunhide_all().

Parameters

• edge_names (list) – list of edge names



Returns

’‘

Return type str

Raises

• CyError – if edge or network name doesn’t exist





Examples

>>> hide_edges(get_edge_names())>>> ''>>> hide_edges(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], network=→˓'galFiltered.sif')>>> ''

See also:

set_edge_property_bypass(), hide_edges(), unhide_edges(), unhide_all()

py4cytoscape.style_bypasses.hide_selected_edges

hide_selected_edges(network=None, base_url='http://localhost:1234/v1')Hide Selected Edges.

Hide (but do not delete) the currently selected edges, by setting the Visible property bypass value to false.

This method permanently overrides any default values or mappings defined for this visual property of the edgeor edges specified. This method ultimately calls the generic function, set_edge_property_bypass(),which can be used to set any visual property. To restore defaults and mappings, use unhide_edges() orunhide_all().

Parameters



Returns

’‘

Return type str

Raises



Examples

>>> hide_selected_edges()>>> ''>>> hide_selected_edges(network='galFiltered.sif')>>> ''

See also:

set_edge_property_bypass(), hide_edges(), unhide_edges(), unhide_all()

5.3. Reference 133



py4cytoscape.style_bypasses.set_edge_color_bypass

set_edge_color_bypass(edge_names, new_colors, network=None,base_url='http://localhost:1234/v1')

Set the bypass value for fill color for the specified edge or edges.

This method permanently overrides any default values or mappings defined for this visualproperty of the edge or edges specified. This method ultimately calls the generic function,set_edge_property_bypass() which can be used to set any visual property. To restore defaultsand mappings, use clear_edge_property_bypass(), see examples.

Parameters






Return type str

Raises



Examples

>>> set_edge_color_bypass(get_edge_names(), '#FF00FF')>>> ''>>> set_edge_color_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], ['→˓#FF00FF', '#CCCCCC'], network='galFiltered.sif')>>> ''

See also:

set_edge_property_bypass(), clear_edge_property_bypass()

py4cytoscape.style_bypasses.set_edge_font_face_bypass

set_edge_font_face_bypass(edge_names, new_fonts, network=None,base_url='http://localhost:1234/v1')

Override the font face for particular edges.


Parameters





• new_fonts (str or list) – list of font values or single value



Returns

’‘

Return type str

Raises



Examples

>>> set_edge_font_face_bypass(get_edge_names(), 'Dialog.italic,plain,20')>>> ''>>> set_edge_font_face_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], [→˓'Dialog.italic,plain,20', 'Dialog.bold,plain,10'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_font_size_bypass

set_edge_font_size_bypass(edge_names, new_sizes, network=None,base_url='http://localhost:1234/v1')

Override the font size for particular edges.


Parameters


• new_sizes (int or float or list) – list of font sizes or single value



5.3. Reference 135




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_font_size_bypass(get_edge_names(), 20)>>> ''>>> set_edge_font_size_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'],→˓[50, 100], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_label_bypass

set_edge_label_bypass(edge_names, new_labels, network=None,base_url='http://localhost:1234/v1')

Override the label for particular edges.


Parameters


• new_labels (str or list) – list of label values or single value



Returns

’‘

Return type str

Raises






Examples

>>> set_edge_label_bypass(get_edge_names(), 'test label')>>> ''>>> set_edge_label_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], ['A',→˓'B'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_label_color_bypass

set_edge_label_color_bypass(edge_names, new_colors, network=None,base_url='http://localhost:1234/v1')

Override the label color for particular edges.


Parameters






Return type str

Raises



Examples

>>> set_edge_label_color_bypass(get_edge_names(), '#FF00FF')>>> ''>>> set_edge_label_color_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'],→˓['#FF00FF', '#FFFF00'], network='galFiltered.sif')>>> ''

See also:


5.3. Reference 137



py4cytoscape.style_bypasses.set_edge_label_opacity_bypass

set_edge_label_opacity_bypass(edge_names, new_values, network=None,base_url='http://localhost:1234/v1')

Override the label opacity for particular edges.


Parameters






Return type str

Raises



Examples

>>> set_edge_label_opacity_bypass(get_edge_names(), '#FF00FF')>>> ''>>> set_edge_label_opacity_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C→˓'], [128, 192], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_line_style_bypass

set_edge_line_style_bypass(edge_names, new_styles, network=None,base_url='http://localhost:1234/v1')

Override the style for particular edges.


Parameters





• new_styles (str or list) – List of styles, or single value.




Return type str

Raises



Examples

>>> set_edge_shape_bypass(get_edge_names(), 'SOLID')>>> ''>>> set_edge_shape_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], [→˓'SOLID', 'ZIGZAG'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_line_width_bypass

set_edge_line_width_bypass(edge_names, new_widths, network=None,base_url='http://localhost:1234/v1')

Override the width for particular edges.


Parameters


• new_widths (int or float or list) – list of width values or single value



Returns ‘’ (None if width is invalid)

Return type str

5.3. Reference 139




Raises



Examples

>>> set_edge_width_bypass(get_edge_names(), 80)>>> ''>>> set_edge_width_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], [80,→˓100.5], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_opacity_bypass

set_edge_opacity_bypass(edge_names, new_values, network=None,base_url='http://localhost:1234/v1')

Override the opacity for particular edges.

This method permanently overrides any default values or mappings defined for this visualproperty of the node or nodes specified. This method ultimately calls the generic function,set_edge_property_bypass() which can be used to set any visual property. To restore defaultsand mappings, use clear_edge_property_bypass(), see examples.

Parameters






Return type str

Raises






Examples

>>> set_edge_opacity_bypass(get_edge_names(), 128)>>> ''>>> set_edge_opacity_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'],→˓[128, 192], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_source_arrow_color_bypass

set_edge_source_arrow_color_bypass(edge_names, new_colors, network=None,base_url='http://localhost:1234/v1')



Parameters






Return type str

Raises



Examples


See also:


5.3. Reference 141



py4cytoscape.style_bypasses.set_edge_source_arrow_shape_bypass

set_edge_source_arrow_shape_bypass(edge_names, new_shapes, network=None,base_url='http://localhost:1234/v1')

Override the source arrow shape for particular edges.


Parameters


• new_shapes (str or list) – List of styles, or single value.




Return type str

Raises



Examples

>>> set_edge_source_arrow_shape_bypass(get_edge_names(), 'ARROW')>>> ''>>> set_edge_source_arrow_shape_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp)→˓YNR050C'], ['DIAMOND', 'CIRCLE'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_target_arrow_color_bypass

set_edge_target_arrow_color_bypass(edge_names, new_colors, network=None,base_url='http://localhost:1234/v1')



Parameters









Return type str

Raises



Examples


See also:


py4cytoscape.style_bypasses.set_edge_target_arrow_shape_bypass

set_edge_target_arrow_shape_bypass(edge_names, new_shapes, network=None,base_url='http://localhost:1234/v1')

Override the target arrow shape for particular edges.


Parameters


• new_shapes (str or list) – List of styles, or single value.




Return type str

5.3. Reference 143




Raises



Examples

>>> set_edge_target_arrow_shape_bypass(get_edge_names(), 'ARROW')>>> ''>>> set_edge_target_arrow_shape_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp)→˓YNR050C'], ['DIAMOND', 'CIRCLE'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.set_edge_tooltip_bypass

set_edge_tooltip_bypass(edge_names, new_tooltip, network=None,base_url='http://localhost:1234/v1')

Sets a bypass tooltip for one or more edges.


Parameters


• new_tooltip (str or list) – list of size values or single value



Returns

’‘

Return type str

Raises






Examples

>>> set_edge_tooltip_bypass(get_edge_names(), 'Some Tooltip')>>> ''>>> set_edge_tooltip_bypass(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], [→˓'One Tooltip', 'Other Tooltip'], network='galFiltered.sif')>>> ''

See also:


py4cytoscape.style_bypasses.unhide_edges

unhide_edges(edge_names, network=None, base_url='http://localhost:1234/v1')Unhide Edges.

Unhide specified edges that were previously hidden, by clearing the edge Visible property bypass value.

This method ultimately calls the generic function, clear_edge_property_bypass(), which can be usedto clear any visual property.

Parameters





Return type dict

Raises



Examples

>>> hide_edges(get_edge_names())>>> ''>>> hide_edges(['YJR022W (pp) YNL050C', 'YJR022W (pp) YNR050C'], network=→˓'galFiltered.sif')>>> ''

See also:

clear_edge_property_bypass(), unhide_all()

5.3. Reference 145



Network Style Bypasses

clear_network_center_bypass([network,base_url])

Clear the bypass value for center x and y for the net-work, effectively restoring prior default values.

clear_network_property_bypass(visual_property)Clear Network Property Bypass.clear_network_zoom_bypass([network,base_url])

Clear the bypass value for the scale factor for the net-work, effectively restoring prior default values.

set_network_center_bypass(x, y[, bypass,. . . ])

Set the bypass value for center x and y for the network.

set_network_property_bypass(new_value,. . . )

Set Network Property Bypass.

set_network_zoom_bypass(new_value[, bypass,. . . ])

Set the bypass value for scale factor for the network.

unhide_all([network, base_url]) Unhide all previously hidden nodes and edges, by clear-ing the Visible property bypass value.

py4cytoscape.style_bypasses.clear_network_center_bypass

clear_network_center_bypass(network=None, base_url='http://localhost:1234/v1')Clear the bypass value for center x and y for the network, effectively restoring prior default values.

Parameters




Return type dict

Raises

• CyError – if center property or network name doesn’t exist


Examples

>>> clear_network_center_bypass()>>> {'data': {}, 'errors': []}>>> clear_network_center_bypass(network='galFiltered.sif')>>> {'data': {}, 'errors': []}

Warning: Before clearing the center coordinate bypass, the coordinate bypass must have been set viaa call to either set_network_center_bypass() or set_network_property_bypass() withthe bypass=True parameter set. Otherwise, clearing this property will throw an exception.




py4cytoscape.style_bypasses.clear_network_property_bypass

clear_network_property_bypass(visual_property, network=None,base_url='http://localhost:1234/v1')

Clear Network Property Bypass.

Clear bypass values for any network property, effectively restoring any previously defined style defaults ormappings.

Parameters






Return type dict

Raises

• CyError – if visual property or network name doesn’t exist


Examples

>>> clear_network_property_bypass('NETWORK_SCALE_FACTOR')>>> ''>>> clear_network_property_bypass('NETWORK_SCALE_FACTOR', network='galFiltered.sif→˓')>>> ''

See also:

set_network_property_bypass()

py4cytoscape.style_bypasses.clear_network_zoom_bypass

clear_network_zoom_bypass(network=None, base_url='http://localhost:1234/v1')Clear the bypass value for the scale factor for the network, effectively restoring prior default values.

Parameters



5.3. Reference 147





Return type dict

Raises

• CyError – if zoom property or network name doesn’t exist


Examples

>>> clear_network_zoom_bypass()>>> {'data': {}, 'errors': []}>>> clear_network_zoom_bypass(network='galFiltered.sif')>>> {'data': {}, 'errors': []}

Warning: Before clearing the zoom bypass, the zoom bypass must have been set via a call to eitherset_network_zoom_bypass() or set_network_property_bypass() with the bypass=Trueparameter set. Otherwise, clearing this property will throw an exception.

py4cytoscape.style_bypasses.set_network_center_bypass

set_network_center_bypass(x, y, bypass=False, network=None,base_url='http://localhost:1234/v1')

Set the bypass value for center x and y for the network.

This function could be used to pan and scroll the Cytoscape canvas.

This method permanently overrides any default values for this visual property. This method ultimately calls thegeneric function, set_network_property_bypass(), which can be used to set any visual property. Torestore defaults, use clear_network_property_bypass().

Parameters

• x (float) – Coordinate value, increases going to the right.

• y (float) – Coordinate value, increases going to the down.

• bypass (bool) – Whether to set permanent bypass value. Default is False per commonuse of temporary zoom settings.



Returns

’‘

Return type str

Raises






Examples

>>> set_network_center_bypass(1.5, bypass=True)>>> ''>>> set_network_center_bypass(0.25, bypass=True, network='galFiltered.sif')>>> ''

See also:

set_network_property_bypass(), clear_netowrk_property_bypass()

py4cytoscape.style_bypasses.set_network_property_bypass

set_network_property_bypass(new_value, visual_property, bypass=True, network=None,base_url='http://localhost:1234/v1')

Set Network Property Bypass.

Set bypass values for any network property, overriding default values defined by any visual style.

This method permanently overrides any default values or mappings defined for the visual properties of thenetwork specified. To restore defaults and mappings, use clear_network_property_bypass().

Parameters

• new_value (any) – Value to set





Returns

’‘

Return type str

Raises

• CyError – if visual property or network name doesn’t exist


5.3. Reference 149



Examples

>>> set_network_property_bypass(0.5, 'NETWORK_SCALE_FACTOR')>>> ''>>> set_network_property_bypass(0.5, 'NETWORK_SCALE_FACTOR', network='galFiltered.→˓sif')>>> ''

See also:

clear_network_property_bypass()

py4cytoscape.style_bypasses.set_network_zoom_bypass

set_network_zoom_bypass(new_value, bypass=False, network=None,base_url='http://localhost:1234/v1')

Set the bypass value for scale factor for the network.

This method permanently overrides any default values for this visual property. This method ultimately calls thegeneric function, set_network_property_bypass(), which can be used to set any visual property. Torestore defaults, use clear_network_property_bypass().

Parameters

• new_value (float) – Zoom factor

• bypass (bool) – Whether to set permanent bypass value. Default is False per commonuse of temporary zoom settings.



Returns

’‘

Return type str

Raises



Examples

>>> set_network_zoom_bypass(1.5, bypass=True)>>> ''>>> set_network_zoom_bypass(0.25, bypass=True, network='galFiltered.sif')>>> ''

See also:

set_network_property_bypass(), clear_netowrk_property_bypass()




py4cytoscape.style_bypasses.unhide_all

unhide_all(network=None, base_url='http://localhost:1234/v1')Unhide all previously hidden nodes and edges, by clearing the Visible property bypass value.

Parameters



Returns

’‘

Return type str

Raises



Examples

>>> unhide_all()>>> ''>>> unhide_all(network='galFiltered.sif')>>> ''

See also:

clear_edge_property_bypass(), unhide_nodes(), unhide_edges()

Style Defaults

Functions for getting and setting DEFAULT values for visual properties, organized into sections:

I. General functions for setting node, edge and network defaults

II. Specific functions for setting particular node, edge and network defaults

General Style Defaults

get_visual_property_default(property[,. . . ])

Retrieve the default value for a visual property.

set_visual_property_default(style_string[,. . . ])

Set the default value for a visual property.

update_style_defaults(style_name, defaults) Update the default values of visual properties in a style.

5.3. Reference 151



py4cytoscape.style_defaults.get_visual_property_default

get_visual_property_default(property, style_name='default', base_url='http://localhost:1234/v1')Retrieve the default value for a visual property.

Parameters

• property (str) – Name of property, e.g., NODE_FILL_COLOR (seeget_visual_property_names)

• style_name (str) – Name of style; default is “default” style


Returns

’‘

Return type str

Raises

• CyError – if style name doesn’t exist


Examples

>>> get_visual_property_default('EDGE_UNSELECTED_PAINT')''>>> get_visual_property_default('NODE_SHAPE', style_name='galFiltered Style')''

py4cytoscape.style_defaults.set_visual_property_default

set_visual_property_default(style_string, style_name='default', base_url='http://localhost:1234/v1')Set the default value for a visual property.

Parameters

• style_string (dict) – The name and value for the property as {‘visualProperty’:‘NODE_SIZE’, ‘value’: ‘35’}



Returns

’‘

Return type str

Raises

• CyError – if property or style name doesn’t exist






Examples

>>> set_visual_property_default({'visualProperty': 'EDGE_UNSELECTED_PAINT', 'value→˓': '#CCCCCC'}, style_name='galFiltered Style')''>>> set_visual_property_default({'visualProperty': 'EDGE_TARGET_ARROW_SHAPE',→˓'value': 'CIRCLE'})''

py4cytoscape.style_defaults.update_style_defaults

update_style_defaults(style_name, defaults, base_url='http://localhost:1234/v1')Update the default values of visual properties in a style.

Updates visual property defaults, overriding any prior settings. See map_visual_property() for the listof visual properties.

Parameters


• defaults (dict) – a dict of visual property default settings


Returns

’‘

Return type str

Raises



Examples

>>> update_style_defaults('galFiltered Style', {'edge width': '50.0', 'EDGE_→˓TARGET_ARROW_SHAPE': 'CIRCLE'})''>>> update_style_defaults(defaults={'node shape': 'OCTAGON', 'EDGE_LINE_TYPE':→˓'ZIGZAG'})''

See also:

map_visual_property()

5.3. Reference 153



Custom Graphics

remove_node_custom_graphics([slot, . . . ]) Remove Node Custom Graphics.set_node_custom_bar_chart(columns[, type,. . . ])

Set Node Custom Bar Chart.

set_node_custom_box_chart(columns[, colors,. . . ])

Set Node Custom Box Chart.

set_node_custom_heat_map_chart(columns[,. . . ])

Set Node Custom HeatMap Chart.

set_node_custom_line_chart(columns[, . . . ]) Set Node Custom Line Chart.set_node_custom_linear_gradient([colors,. . . ])

Set Node Custom Linear Gradient.

set_node_custom_pie_chart(columns[, colors,. . . ])

Set Node Custom Pie Chart.

set_node_custom_position([node_anchor,. . . ])

Set Node Custom Position.

set_node_custom_radial_gradient([colors,. . . ])

Set Node Custom Radial Gradient.

set_node_custom_ring_chart(columns[, . . . ]) Set Node Custom Ring Chart.

py4cytoscape.style_defaults.remove_node_custom_graphics

remove_node_custom_graphics(slot=1, style_name='default', base_url='http://localhost:1234/v1')Remove Node Custom Graphics.

Remove the default custom charts, images and gradients.

Parameters

• slot (int) – Which custom graphics slot to modify. Slots 1-9 are available for indepen-dent charts, gradients and images. Default is 1.



Returns

’‘

Return type str

Raises

• CyError – if style name or slot doesn’t exist





Examples

>>> remove_node_custom_graphics(style_name='galFiltered Style')''>>> remove_node_custom_graphics(slot=2, style_name='galFiltered Style')''

py4cytoscape.style_defaults.set_node_custom_bar_chart

set_node_custom_bar_chart(columns, type='GROUPED', colors=None, range=None, ori-entation='VERTICAL', col_axis=False, range_axis=False,zero_line=False, axis_width=0.25, axis_color='#000000',axis_font_size=1, separation=0.0, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Bar Chart.

Makes a bar chart per node using specified node table columns by setting a default custom graphic style.

Parameters

• columns (list) – List of node column names to be displayed, in order.

• type (str) – Type of bar chart: GROUPED (default), STACKED, HEAT_STRIPS, orUP_DOWN

• colors (list) – List of colors to be matched with columns or with range, depending ontype. Default is a set of colors from an appropriate Brewer palette.

• range (list) – Min and max values of chart. Default is to use min and max from specifieddata columns.

• orientation (str) – HORIZONTAL or VERTICAL (default).

• col_axis (bool) – Show axis with column labels. Default is False.

• range_axis (bool) – Show axis with range of values. Default is False.

• zero_line (book) – Show a line at zero. Default is False.

• axis_width (float) – Width of axis lines, if shown. Default is 0.25.

• axis_color (str) – Color of axis lines, if shown. Default is black (‘#000000’).

• axis_font_size (int) – Font size of axis labels, if shown. Default is 1.

• separation (float) – Distance between bars. Default is 0.0.




Returns

’‘

Return type str

Raises

5.3. Reference 155



• CyError – if style name, chart type or slot doesn’t exist


Examples

>>> set_node_custom_bar_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓style_name='galFiltered Style')''>>> set_node_custom_bar_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓colors=['#FF00FF', '#00FF00'], slot=2, style_name='galFiltered Style')''

See also:

set_node_custom_position(), remove_node_custom_graphics()

py4cytoscape.style_defaults.set_node_custom_box_chart

set_node_custom_box_chart(columns, colors=None, range=None, orientation='VERTICAL',range_axis=False, zero_line=False, axis_width=0.25,axis_color='#000000', axis_font_size=1, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Box Chart.

Makes a box chart per node using specified node table columns by setting a default custom graphic style.

Parameters




• orientation (str) – HORIZONTAL or VERTICAL (default).

• col_axis (bool) – Show axis with column labels. Default is False.












Returns

’‘

Return type str

Raises



Examples

>>> set_node_custom_box_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓style_name='galFiltered Style')''>>> set_node_custom_box_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓colors=['#FF00FF', '#00FF00'], slot=2, style_name='galFiltered Style')''

See also:


py4cytoscape.style_defaults.set_node_custom_heat_map_chart

set_node_custom_heat_map_chart(columns, colors=None, range=None, ori-entation='HORIZONTAL', range_axis=False,zero_line=False, axis_width=0.25, axis_color='#000000',axis_font_size=1, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom HeatMap Chart.

Makes a heat map per node using specified node table columns by setting a default custom graphic style.

Parameters




• orientation (str) – HORIZONTAL (default) or VERTICAL.







5.3. Reference 157




Returns

’‘

Return type str

Raises



Examples

>>> set_node_custom_heat_map_chart(['AverageShortestPath', 'BetweennessCentrality→˓'], style_name='galFiltered Style')''>>> set_node_custom_heat_map_chart(['AverageShortestPath', 'BetweennessCentrality→˓'], colors=['#123456', '#654321', '#112233', '#888888'], slot=2, style_name=→˓'galFiltered Style')''

See also:


py4cytoscape.style_defaults.set_node_custom_line_chart

set_node_custom_line_chart(columns, colors=None, range=None, line_width=1.0,range_axis=False, zero_line=False, axis_width=0.25,axis_color='#000000', axis_font_size=1, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Line Chart.

Makes a line chart per node using specified node table columns by setting a default custom graphic style.

Parameters




• line_width (float) – Width of chart line. Default is 1.0.












Returns

’‘

Return type str

Raises



Examples

>>> set_node_custom_line_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓style_name='galFiltered Style')''>>> set_node_custom_line_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓colors=['#FF00FF', '#00FF00'], slot=2, style_name='galFiltered Style')''

See also:


py4cytoscape.style_defaults.set_node_custom_linear_gradient

set_node_custom_linear_gradient(colors=['#DDDDDD', '#888888'], anchors=[0.0,1.0], angle=0.0, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Linear Gradient.

Makes a gradient fill per node by setting a default custom graphic style.

Parameters

• colors (list) – List of colors to define gradient

• anchors (list) – Position of colors from 0.0 to 1.0.

• angle (float) – Angle of gradient. Default is 0 (left-to-right).




5.3. Reference 159




Returns

’‘

Return type str

Raises



Examples

>>> set_node_custom_linear_gradient(style_name='galFiltered Style')''>>> set_node_custom_linear_gradient(colors=['#FF00FF', '#00FF00'], angle=90.0,→˓slot=2, style_name='galFiltered Style')''

py4cytoscape.style_defaults.set_node_custom_pie_chart

set_node_custom_pie_chart(columns, colors=None, start_angle=0.0, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Pie Chart.

Makes a pie chart per node using specified node table columns by setting a default custom graphic style.

Parameters



• start_angle (float) – Angle to start filling pie. Default is 0.0.




Returns

’‘

Return type str

Raises






Examples

>>> set_node_custom_pie_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓style_name='galFiltered Style')''>>> set_node_custom_pie_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓colors=['#FF00FF', '#00FF00'], slot=2, style_name='galFiltered Style')''

See also:


py4cytoscape.style_defaults.set_node_custom_position

set_node_custom_position(node_anchor='C', graphic_anchor='C', justification='C',x_offset=0.0, y_offset=0.0, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Position.

Adjust the position of a custom graphic relative to its node.

Parameters

• node_anchor (str) – Position on node to place the graphic: NW,N,NE,E,SE,S,SW,Wor C for center (default)

• graphic_anchor (str) – Position on graphic to place on node:NW,N,NE,E,SE,S,SW,W or C for center (default)

• justification (str) – Positioning of content within graphic: l,r,c (default)

• x_offset (float) – Additional offset in the x direction

• y_offset (float) – Additional offset in the y direction




Returns

’‘

Return type str

Raises



5.3. Reference 161



Examples

>>> set_node_custom_position(node_anchor='W', graphic_anchor='E', style_name=→˓'galFiltered Style')''>>> set_node_custom_position(justification='l', slot=2, style_name='galFiltered→˓Style')''

py4cytoscape.style_defaults.set_node_custom_radial_gradient

set_node_custom_radial_gradient(colors=['#DDDDDD', '#888888'], anchors=[0.0, 1.0],x_center=0.5, y_center=0.5, slot=1, style_name='default',base_url='http://localhost:1234/v1')

Set Node Custom Radial Gradient.

Makes a gradient fill per node by setting a default custom graphic style.

Parameters

• colors (list) – List of colors to define gradient

• anchors (list) – Position of colors from 0.0 to 1.0.

• x_center (float) – X position for center of radial effect from 0.0 to 1.0. Default is 0.5.

• y_center (float) – Y position for center of radial effect from 0.0 to 1.0. Default is 0.5.




Returns

’‘

Return type str

Raises






Examples

>>> set_node_custom_radial_gradient(style_name='galFiltered Style')''>>> set_node_custom_radial_gradient(colors=['#FF00FF', '#00FF00'], x_center=0.0,→˓y_center=0.0, slot=2, style_name='galFiltered Style')''

py4cytoscape.style_defaults.set_node_custom_ring_chart

set_node_custom_ring_chart(columns, colors=None, start_angle=0.0, hole_size=0.5, slot=1,style_name='default', base_url='http://localhost:1234/v1')

Set Node Custom Ring Chart.

Makes a ring chart per node using specified node table columns by setting a default custom graphic style.

Parameters


• colors (list) – List of colors to be matched with columns or with

• start_angle (float) – Angle to start filling ring. Default is 0.0.

• hole_size (float) – Size of hole in ring. Ranges 0-1. Default is 0.5.




Returns

’‘

Return type str

Raises



Examples

>>> set_node_custom_ring_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓style_name='galFiltered Style')''>>> set_node_custom_ring_chart(['AverageShortestPath', 'BetweennessCentrality'],→˓colors=['#FF00FF', '#00FF00'], slot=2, style_name='galFiltered Style')''

See also:


5.3. Reference 163



Node Style Defaults

get_node_selection_color_default([. . . ]) Retrieve the default selection node color.set_node_border_color_default(new_color[,. . . ])

Set the default node border color.

set_node_border_opacity_default(new_opacity)Set defaults opacity value for all unmapped node bor-ders.

set_node_border_width_default(new_width[,. . . ])

Set the default node border width.

set_node_color_default(new_color[, . . . ]) Set the default node color.set_node_fill_opacity_default(new_opacity[,. . . ])

Set default opacity value for all unmapped nodes.

set_node_font_face_default(new_font[,. . . ])

Set the default node font.

set_node_font_size_default(new_size[,. . . ])

Set the default node font size.

set_node_height_default(new_height[, . . . ]) Set the default node height.set_node_label_color_default(new_color[,. . . ])

Set the default node label color.

set_node_label_default(new_label[, . . . ]) Set the default node label.set_node_label_opacity_default(new_opacity)Set default opacity value for all unmapped node labels.set_node_selection_color_default(new_color)Set the default node border color.set_node_shape_default(new_shape[, . . . ]) Set the default node shape.set_node_size_default(new_size[, . . . ]) Set the default node font size.set_node_tooltip_default(new_tooltip[, . . . ]) Set the default node tooltip.set_node_width_default(new_width[, . . . ]) Set the default node width.

py4cytoscape.style_defaults.get_node_selection_color_default

get_node_selection_color_default(style_name='default', base_url='http://localhost:1234/v1')Retrieve the default selection node color.

Parameters



Returns

’‘

Return type str

Raises






Examples

>>> get_node_selection_color_default(style_name='galFiltered Style')''>>> get_node_selection_color_default()''

py4cytoscape.style_defaults.set_node_border_color_default

set_node_border_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')


Parameters

• new_color (str) – color as hex code, e.g., #FD5903



Returns

’‘

Return type str

Raises



Examples

>>> set_node_border_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_node_border_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_node_border_opacity_default

set_node_border_opacity_default(new_opacity, style_name='default',base_url='http://localhost:1234/v1')

Set defaults opacity value for all unmapped node borders.

Parameters

• new_opacity (int) – Numeric values between 0 and 255; 0 is invisible.



5.3. Reference 165




Returns

’‘

Return type str

Raises



Examples

>>> set_node_border_opacity_default(205, style_name='galFiltered Style')''>>> set_node_border_opacity_default(10)''

py4cytoscape.style_defaults.set_node_border_width_default

set_node_border_width_default(new_width, style_name='default',base_url='http://localhost:1234/v1')

Set the default node border width.

Parameters

• new_width (int) – Numeric value for width



Returns

’‘

Return type str

Raises






Examples

>>> set_node_border_width_default(25, style_name='galFiltered Style')''>>> set_node_border_width_default(10)''

py4cytoscape.style_defaults.set_node_color_default

set_node_color_default(new_color, style_name='default', base_url='http://localhost:1234/v1')Set the default node color.

Parameters




Returns

’‘

Return type str

Raises



Examples

>>> set_node_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_node_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_node_fill_opacity_default

set_node_fill_opacity_default(new_opacity, style_name='default',base_url='http://localhost:1234/v1')

Set default opacity value for all unmapped nodes.

Parameters




5.3. Reference 167




Returns

’‘

Return type str

Raises



Examples

>>> set_node_fill_opacity_default(205, style_name='galFiltered Style')''>>> set_node_fill_opacity_default(10)''

py4cytoscape.style_defaults.set_node_font_face_default

set_node_font_face_default(new_font, style_name='default', base_url='http://localhost:1234/v1')Set the default node font.

Parameters

• new_font (str) – String specification of font face, style and size, e.g., ‘“SansSerif,plain,12” or “Dialog,plain,10”



Returns

’‘

Return type str

Raises






Examples

>>> set_node_font_face_default('Dialog.italic,plain,12', style_name='galFiltered→˓Style')''>>> set_node_font_face_default('Dialog.italic,plain,12')''

py4cytoscape.style_defaults.set_node_font_size_default

set_node_font_size_default(new_size, style_name='default', base_url='http://localhost:1234/v1')Set the default node font size.

Parameters

• new_size (int) – Numeric value for size



Returns

’‘

Return type str

Raises



Examples

>>> set_node_font_size_default(20, style_name='galFiltered Style')''>>> set_node_font_size_default(20)''

py4cytoscape.style_defaults.set_node_height_default

set_node_height_default(new_height, style_name='default', base_url='http://localhost:1234/v1')Set the default node height.

Parameters

• new_height (int) – Numeric value for height.



5.3. Reference 169




Returns

’‘

Return type str

Raises



Examples

>>> set_node_height_default(20, style_name='galFiltered Style')''>>> set_node_height_default(20)''

py4cytoscape.style_defaults.set_node_label_color_default

set_node_label_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default node label color.

Parameters




Returns

’‘

Return type str

Raises






Examples

>>> set_node_label_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_node_label_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_node_label_default

set_node_label_default(new_label, style_name='default', base_url='http://localhost:1234/v1')Set the default node label.

Parameters

• new_label (str) – String label for unmapped nodes.



Returns

’‘

Return type str

Raises



Examples

>>> set_node_label_default('test label', style_name='galFiltered Style')''>>> set_node_label_default('test label')''

py4cytoscape.style_defaults.set_node_label_opacity_default

set_node_label_opacity_default(new_opacity, style_name='default',base_url='http://localhost:1234/v1')

Set default opacity value for all unmapped node labels.

Parameters




5.3. Reference 171




Returns

’‘

Return type str

Raises



Examples

>>> set_node_label_opacity_default(50, style_name='galFiltered Style')''>>> set_node_label_opacity_default(50)''

py4cytoscape.style_defaults.set_node_selection_color_default

set_node_selection_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')


Parameters




Returns

’‘

Return type str

Raises






Examples

>>> set_node_selection_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_node_selection_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_node_shape_default

set_node_shape_default(new_shape, style_name='default', base_url='http://localhost:1234/v1')Set the default node shape.

Parameters

• new_shape (str) – Name of shape, e.g., ELLIPSE, RECTANGLE, etc (seeget_node_shapes())



Returns

’‘

Return type str

Raises



Examples

>>> set_node_shape_default('ELLIPSE', style_name='galFiltered Style')''>>> set_node_shape_default('ELLIPSE')''

py4cytoscape.style_defaults.set_node_size_default

set_node_size_default(new_size, style_name='default', base_url='http://localhost:1234/v1')Set the default node font size.

Parameters




5.3. Reference 173




Returns

’‘

Return type str

Raises



Examples

>>> set_node_size_default(20, style_name='galFiltered Style')''>>> set_node_size_default(20)''

py4cytoscape.style_defaults.set_node_tooltip_default

set_node_tooltip_default(new_tooltip, style_name='default', base_url='http://localhost:1234/v1')Set the default node tooltip.

Parameters

• new_tooltip (str) – String tooltip for unmapped nodes.



Returns

’‘

Return type str

Raises



Examples

>>> set_node_tooltip_default('test tooltip', style_name='galFiltered Style')''>>> set_node_tooltip_default('test tooltip')''




py4cytoscape.style_defaults.set_node_width_default

set_node_width_default(new_width, style_name='default', base_url='http://localhost:1234/v1')Set the default node width.

Parameters

• new_width (int) – Numeric value for width



Returns

’‘

Return type str

Raises



Examples

>>> set_node_width_default(20, style_name='galFiltered Style')''>>> set_node_width_default(20)''

Edge Style Defaults

get_edge_selection_color_default([. . . ]) Retrieve the default selected edge color.set_edge_color_default(new_color[, . . . ]) Set the default edge color.set_edge_font_face_default(new_font[,. . . ])

Set the default edge font.

set_edge_font_size_default(new_size[,. . . ])

Set the default edge font size.

set_edge_label_color_default(new_color[,. . . ])

Set the default edge label color.

set_edge_label_default(new_label[, . . . ]) Set the default edge label.set_edge_label_opacity_default(new_opacity)Set default opacity value for all unmapped edges.set_edge_line_style_default(new_line_style) Set the default edge style.set_edge_line_width_default(new_width[,. . . ])

Set the default edge width.

set_edge_opacity_default(new_opacity[,. . . ])

Set default opacity value for all unmapped edges.

set_edge_selection_color_default(new_color)Set the default selected edge color.set_edge_source_arrow_color_default(new_color)Set the default edge source arrow color.


5.3. Reference 175



Table 36 – continued from previous pageset_edge_source_arrow_shape_default(new_shape)Set the default edge source arrow shape.set_edge_target_arrow_color_default(new_color)Set the default edge target arrow color.set_edge_target_arrow_shape_default(new_shape)Set the default edge target arrow shape.set_edge_tooltip_default(new_tooltip[, . . . ]) Set the default edge tooltip.

py4cytoscape.style_defaults.get_edge_selection_color_default

get_edge_selection_color_default(style_name='default', base_url='http://localhost:1234/v1')Retrieve the default selected edge color.

Parameters



Returns

’‘

Return type str

Raises



Examples

>>> get_edge_selection_color_default(style_name='galFiltered Style')''>>> get_edge_selection_color_default()''

py4cytoscape.style_defaults.set_edge_color_default

set_edge_color_default(new_color, style_name='default', base_url='http://localhost:1234/v1')Set the default edge color.

Parameters




Returns

’‘





Return type str

Raises



Examples

>>> set_edge_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_edge_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_edge_font_face_default

set_edge_font_face_default(new_font, style_name='default', base_url='http://localhost:1234/v1')Set the default edge font.

Parameters

• new_font (str) – String specification of font face, style and size, e.g., ‘“SansSerif,plain,12” or “Dialog,plain,10”



Returns

’‘

Return type str

Raises



Examples

>>> set_edge_font_face_default('Dialog.italic,plain,12', style_name='galFiltered→˓Style')''>>> set_edge_font_face_default('Dialog.italic,plain,12')''

5.3. Reference 177



py4cytoscape.style_defaults.set_edge_font_size_default

set_edge_font_size_default(new_size, style_name='default', base_url='http://localhost:1234/v1')Set the default edge font size.

Parameters




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_font_size_default(20, style_name='galFiltered Style')''>>> set_edge_font_size_default(20)''

py4cytoscape.style_defaults.set_edge_label_color_default

set_edge_label_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge label color.

Parameters




Returns

’‘

Return type str

Raises







Examples

>>> set_edge_label_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_edge_label_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_edge_label_default

set_edge_label_default(new_label, style_name='default', base_url='http://localhost:1234/v1')Set the default edge label.

Parameters

• new_label (str) – String label for unmapped edges.



Returns

’‘

Return type str

Raises



Examples

>>> set_node_label_default('test label', style_name='galFiltered Style')''>>> set_node_label_default('test label')''

py4cytoscape.style_defaults.set_edge_label_opacity_default

set_edge_label_opacity_default(new_opacity, style_name='default',base_url='http://localhost:1234/v1')

Set default opacity value for all unmapped edges.

Parameters



5.3. Reference 179




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_label_opacity_default(205, style_name='galFiltered Style')''>>> set_edge_label_opacity_default(10)''

py4cytoscape.style_defaults.set_edge_line_style_default

set_edge_line_style_default(new_line_style, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge style.

Parameters

• new_line_style (str) – Name of line style, e.g., SOLID, LONG_DASH, etc (seeget_line_styles())



Returns

’‘

Return type str

Raises







Examples

>>> set_edge_line_width_default('SOLID', style_name='galFiltered Style')''>>> set_edge_line_width_default('ZIGZAG')''

py4cytoscape.style_defaults.set_edge_line_width_default

set_edge_line_width_default(new_width, style_name='default', base_url='http://localhost:1234/v1')Set the default edge width.

Parameters

• new_width (int) – Numeric value for width.



Returns

’‘

Return type str

Raises



Examples

>>> set_edge_line_width_default(20, style_name='galFiltered Style')''>>> set_edge_line_width_default(10)''

py4cytoscape.style_defaults.set_edge_opacity_default

set_edge_opacity_default(new_opacity, style_name='default', base_url='http://localhost:1234/v1')Set default opacity value for all unmapped edges.

Parameters




5.3. Reference 181




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_opacity_default(205, style_name='galFiltered Style')''>>> set_edge_opacity_default(10)''

py4cytoscape.style_defaults.set_edge_selection_color_default

set_edge_selection_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default selected edge color.

Parameters




Returns

’‘

Return type str

Raises






Examples

>>> set_edge_selection_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_edge_selection_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_edge_source_arrow_color_default

set_edge_source_arrow_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge source arrow color.

Parameters




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_source_arrow_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_edge_source_arrow_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_edge_source_arrow_shape_default

set_edge_source_arrow_shape_default(new_shape, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge source arrow shape.

Parameters

• new_shape (str) – Name of shape, e.g., ARROW, T, etc (see get_arrow_shapes())



5.3. Reference 183




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_source_arrow_shape_default('ARROW', style_name='galFiltered Style')''>>> set_edge_source_arrow_shape_default('ARROW')''

py4cytoscape.style_defaults.set_edge_target_arrow_color_default

set_edge_target_arrow_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge target arrow color.

Parameters




Returns

’‘

Return type str

Raises






Examples

>>> set_edge_target_arrow_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_edge_target_arrow_color_default('#CCCCCC')''

py4cytoscape.style_defaults.set_edge_target_arrow_shape_default

set_edge_target_arrow_shape_default(new_shape, style_name='default',base_url='http://localhost:1234/v1')

Set the default edge target arrow shape.

Parameters

• new_shape (str) – Name of shape, e.g., ARROW, T, etc (see get_arrow_shapes())



Returns

’‘

Return type str

Raises



Examples

>>> set_edge_target_arrow_shape_default('ARROW', style_name='galFiltered Style')''>>> set_edge_target_arrow_shape_default('ARROW')''

py4cytoscape.style_defaults.set_edge_tooltip_default

set_edge_tooltip_default(new_tooltip, style_name='default', base_url='http://localhost:1234/v1')Set the default edge tooltip.

Parameters

• new_tooltip (str) – String tooltip for unmapped edges.



5.3. Reference 185




Returns

’‘

Return type str

Raises



Examples

>>> set_edge_tooltip_default('test tooltip', style_name='galFiltered Style')''>>> set_edge_tooltip_default('test tooltip')''

Network Style Defaults

get_background_color_default([style_name,. . . ])

Retrieve the default background color.

set_background_color_default(new_color[,. . . ])

Set the default background color.

py4cytoscape.style_defaults.get_background_color_default

get_background_color_default(style_name='default', base_url='http://localhost:1234/v1')Retrieve the default background color.

Parameters



Returns

’‘

Return type str

Raises






Examples

>>> get_background_color_default(style_name='galFiltered Style')''>>> get_background_color_default()''

py4cytoscape.style_defaults.set_background_color_default

set_background_color_default(new_color, style_name='default',base_url='http://localhost:1234/v1')

Set the default background color.

Parameters




Returns

’‘

Return type str

Raises



Examples

>>> set_background_color_default('#CCCCCC', style_name='galFiltered Style')''>>> set_background_color_default('#CCCCCC')''

Style Dependencies

# Functions for getting and setting style DEPEDENDENCIES, organized into sections:

I. General functions for getting and setting dependencies

II. Specific functions for setting particular dependencies

5.3. Reference 187



General Style Dependencies

get_style_dependencies([style_name,base_url])

Get the values of dependencies in a style.

set_style_dependencies([style_name, . . . ]) Set the values of dependencies in a style, overriding anyprior setting.

py4cytoscape.style_dependencies.get_style_dependencies

get_style_dependencies(style_name='default', base_url='http://localhost:1234/v1')Get the values of dependencies in a style.

Parameters



Returns contains all dependencies and their current boolean value

Return type dict

Raises



Examples

>>> get_style_dependencies(style_name='galFiltered Style'){'arrowColorMatchesEdge': False, 'nodeCustomGraphicsSizeSync': True,→˓'nodeSizeLocked': True}>>> get_style_dependencies(){'arrowColorMatchesEdge': False, 'nodeCustomGraphicsSizeSync': True,→˓'nodeSizeLocked': False}

py4cytoscape.style_dependencies.set_style_dependencies

set_style_dependencies(style_name='default', dependencies={}, base_url='http://localhost:1234/v1')Set the values of dependencies in a style, overriding any prior setting.

Parameters


• dependencies (dict) – A list of style dependencies, see Available Dependenciesbelow. Note: each dependency is set by a boolean, True or False






Returns contains the views property with a value of the current view’s SUID (e.g., {‘views’:[275240]})

Return type dict

Raises



Examples

>>> set_style_dependencies(dependencies={'arrowColorMatchesEdge': True}, style_→˓name='galFiltered Style'){'views': [275240]}>>> get_style_dependencies(dependencies={'arrowColorMatchesEdge': True,→˓'nodeCustomGraphicsSizeSync': False}){'views': [275240]}

Available Dependencies: arrowColorMatchesEdge, nodeCustomGraphicsSizeSync, nodeSizeLocked

Custom Graphics

sync_node_custom_graphics_size(new_state[,. . . ])

Set a boolean value to have the size of custom graphicsmatch that of the node.

py4cytoscape.style_dependencies.sync_node_custom_graphics_size

sync_node_custom_graphics_size(new_state, style_name='default',base_url='http://localhost:1234/v1')

Set a boolean value to have the size of custom graphics match that of the node.

Parameters

• new_state (bool) – Whether to sync node custom graphics size




Return type dict

Raises



5.3. Reference 189



Examples

>>> sync_node_custom_graphics_size(True, style_name='galFiltered Style'){'views': [275240]}>>> sync_node_custom_graphics_size(False){'views': [275240]}

Node Style Dependencies

lock_node_dimensions(new_state[, . . . ]) Set a boolean value to have node width and height fixedto a single size value.

py4cytoscape.style_dependencies.lock_node_dimensions

lock_node_dimensions(new_state, style_name='default', base_url='http://localhost:1234/v1')Set a boolean value to have node width and height fixed to a single size value.

Parameters

• new_state (bool) – Whether to lock node width and height




Return type dict

Raises



Examples

>>> lock_node_dimensions(True, style_name='galFiltered Style'){'views': [275240]}>>> lock_node_dimensions(False){'views': [275240]}




Edge Style Dependencies

match_arrow_color_to_edge(new_state[, . . . ]) Set a boolean value to have arrow shapes share the samecolor as the edge.

py4cytoscape.style_dependencies.match_arrow_color_to_edge

match_arrow_color_to_edge(new_state, style_name='default', base_url='http://localhost:1234/v1')Set a boolean value to have arrow shapes share the same color as the edge.

Parameters

• new_state (bool) – Whether to match arrow color to edge.




Return type dict

Raises



Examples

>>> match_arrow_color_to_edge(True, style_name='galFiltered Style'){'views': [275240]}>>> match_arrow_color_to_edge(False){'views': [275240]}

Style Mappings

Functions for defining MAPPINGS between table column values and visual properties, organized into sections:

I. General functions for creating and applying mappings for node, edge and network properties

II. Specific functions for defining particular node, edge and network properties

5.3. Reference 191



General Style Mappings

delete_style_mapping(style_name, vi-sual_prop)

Delete a specified visual style mapping from specifiedstyle.

get_style_all_mappings(style_name[,base_url])

Fetch all visual property mapping in a style.

get_style_mapping(style_name, visual_prop[,. . . ])

Fetch a visual property mapping in a style.

map_visual_property(visual_prop, . . . [, . . . ]) Create a mapping between an attribute and a visualproperty.

update_style_mapping(style_name, mapping[,. . . ])

Update a visual property mapping in a style.

py4cytoscape.style_mappings.delete_style_mapping

delete_style_mapping(style_name, visual_prop, base_url='http://localhost:1234/v1')Delete a specified visual style mapping from specified style.

Parameters


• visual_prop (str) – name of visual property to delete


Returns ‘’ or None (if property doesn’t exist)

Return type str or None

Raises



Examples

>>> delete_style_mapping('galFiltered Style', 'node label')''

py4cytoscape.style_mappings.get_style_all_mappings

get_style_all_mappings(style_name, base_url='http://localhost:1234/v1')Fetch all visual property mapping in a style.

The property mappings are the same as a dict created by map_visual_property().

Parameters






Returns list of dicts of the type created by map_visual_property()

Return type list

Raises

• CyError – if style or property name doesn’t exist


Examples

>>> get_style_all_mappings('galFiltered Style')[{"mappingType": "passthrough", "mappingColumn": "name", "mappingColumnType":→˓"String", "visualProperty": "NODE_LABEL"},{"mappingType": "passthrough", "mappingColumn": "interaction", "mappingColumnType→˓": "String", "visualProperty": "EDGE_LABEL"}]

See also:


py4cytoscape.style_mappings.get_style_mapping

get_style_mapping(style_name, visual_prop, base_url='http://localhost:1234/v1')Fetch a visual property mapping in a style.

The property mapping is the same as a dict created by map_visual_property().

Parameters


• visual_prop (str) – the name of the visual property


Returns see map_visual_property()

Return type dict

Raises

• CyError – if style or property name doesn’t exist


5.3. Reference 193




Examples

>>> get_style_mapping('galFiltered Style', 'node label'){"mappingType": "passthrough", "mappingColumn": "COMMON", "mappingColumnType":→˓"String", "visualProperty": "NODE_LABEL"}

See also:


py4cytoscape.style_mappings.map_visual_property

map_visual_property(visual_prop, table_column, mapping_type, table_column_values=[], vi-sual_prop_values=[], network=None, base_url='http://localhost:1234/v1')

Create a mapping between an attribute and a visual property.

Generates the appropriate data structure for the “mapping” parameter in update_style_mapping().

The paired list of values must be of the same length or mapping will fail. For gradient mapping, you mayinclude two additional visual_prop_values in the first and last positions to map respectively to valuesless than and greater than those specified in table_column_values. Mapping will also fail if the data typeof table_column_values does not match that of the existing table_column. Note that all importednumeric data are stored as Integers or Doubles in Cytosacpe tables; and character or mixed data are stored asStrings.

Parameters

• visual_prop (str) – name of visual property to map

• table_column (str) – name of table column to map

• mapping_type (str) – continuous, discrete or passthrough (c,d,p)

• table_column_values (list) – list of values paired with visual_prop_values;skip for passthrough mapping

• visual_prop_values (list) – list of values paired with table_column_values;skip for passthrough mapping



Returns {‘mappingType’: type of mapping, ‘mappingColumn’: column to map, ‘mappingColumn-Type’: column data type, ‘visualProperty’: name of property, cargo}

Return type dict

Raises






Examples

>>> map_visual_property('node fill color', 'gal1RGexp', 'c', [-2.426, 0.0, 2.058],→˓ ['#0066CC', '#FFFFFF','#FFFF00']){'mappingType': 'continuous', 'mappingColumn': 'gal1RGexp', 'mappingColumnType':→˓'Double', 'visualProperty': 'NODE_FILL_COLOR', 'points': [{'value': -2.426,→˓'lesser': '#0066CC', 'equal': '#0066CC', 'greater': '#0066CC'}, {'value': 0.0,→˓'lesser': '#FFFFFF', 'equal': '#FFFFFF', 'greater': '#FFFFFF'}, {'value': 2.058,→˓ 'lesser': '#FFFF00', 'equal': '#FFFF00', 'greater': '#FFFF00'}]}>>> map_visual_property('node shape', 'degree.layout', 'd', [1, 2], ['ellipse',→˓'rectangle']){'mappingType': 'discrete', 'mappingColumn': 'degree.layout', 'mappingColumnType→˓': 'Integer', 'visualProperty': 'NODE_SHAPE', 'map': [{'key': 1, 'value':→˓'ellipse'}, {'key': 2, 'value': 'rectangle'}]}>>> map_visual_property('node label', 'COMMON', 'p'){'mappingType': 'passthrough', 'mappingColumn': 'COMMON', 'mappingColumnType':→˓'String', 'visualProperty': 'NODE_LABEL'}

Note: For the return value, mapping type can be ‘continuous’, ‘discrete’ or ‘passthrough’. For themappingColumn, the name of the column. For the mappingColumnType, the Cytoscape data type (Dou-ble, Integer, String, Boolean). For the visualProperty, the canonical name of the visual property. Thecargo depends on the mapping type. For ‘continuous’, it’s a list of way points as ‘points’: [waypoint,waypoint, . . . ] where a waypoint is {‘value’: a Double, ‘lesser’: a color, ‘equal’: a color, ‘greater’: a color}.For ‘discrete’, it’s a list of mappings as ‘map’: [key-value, key-value, . . . ] where a key-value is {‘key’: columndata value, ‘value’: value appropriate for visualProperty}.

See also:

update_style_mapping(), get_visual_property_names()

py4cytoscape.style_mappings.update_style_mapping

update_style_mapping(style_name, mapping, base_url='http://localhost:1234/v1')Update a visual property mapping in a style.

Updates the visual property mapping, overriding any prior mapping. Creates a visual property mappingif it doesn’t already exist in the style. Requires visual property mappings to be previously created, seemap_visual_property().

Parameters


• mapping (dict) – a single visual property mapping, see map_visual_property()


Returns

’‘

Return type str

Raises


5.3. Reference 195



• TypeError – if mapping isn’t a visual property mapping


Examples

>>> update_style_mapping('galFiltered Style', map_visual_property('node label',→˓'name', 'p'))''

See also:


Node Style Mappings

set_node_border_color_mapping(table_column)Map table column values to colors to set the node bordercolor.

set_node_border_opacity_mapping(table_column)Set opacity for node border only.set_node_border_width_mapping(table_column)Map table column values to widths to set the node bor-

der width.set_node_color_mapping(table_column[, . . . ]) Map table column values to colors to set the node fill

color.set_node_combo_opacity_mapping(table_column)Set opacity for node fill, border and label all together.set_node_fill_opacity_mapping(table_column)Set opacity for node fill only.set_node_font_face_mapping(table_column[,. . . ])

Sets font face for node labels.

set_node_font_size_mapping(table_column[,. . . ])

Map table column values to sizes to set the node size.

set_node_height_mapping(table_column[,. . . ])

Map table column values to the node heights.

set_node_label_color_mapping(table_column[,. . . ])

Map table column values to colors to set the node bordercolor.

set_node_label_mapping(table_column[, . . . ]) Pass the values from a table column to display as nodelabels.

set_node_label_opacity_mapping(table_column)Sets opacity for node label only.set_node_shape_mapping(table_column[, . . . ]) Map table column values to shapes to set the node

shape.set_node_size_mapping(table_column[, . . . ]) Map table column values to node sizes.set_node_tooltip_mapping(table_column[,. . . ])

Pass the values from a table column to display as nodetooltips.

set_node_width_mapping(table_column[, . . . ]) Map table column values to the node widths.



py4cytoscape.style_mappings.set_node_border_color_mapping

set_node_border_color_mapping(table_column, table_column_values=None, colors=None, map-ping_type='c', default_color=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to colors to set the node border color.

Parameters

• table_column (str) – Name of Cytoscape table column to map values from

• table_column_values (list) – List of values from Cytoscape table to be used inmapping

• colors (list) – list of hex colors

• mapping_type (str) – continuous, discrete or passthrough (c,d,p); default is continuous

• default_color (str) – Hex color to set as default




Returns ‘’ if successful or None if error


Raises

• CyError – if table column doesn’t exist, table column values doesn’t match values list, orinvalid style name, network or mapping type


Examples

>>> set_node_border_color_mapping('AverageShortestPathLength', [1.0, 16.36], ['→˓#FBE723', '#440256'], style_name='galFiltered Style')''>>> set_node_border_color_mapping('Degree', ['1', '2'], ['#FFFF00', '#00FF00'], 'd→˓', style_name='galFiltered Style')''>>> set_node_border_color_mapping('ColorCol', mapping_type='p', default_color='→˓#654321', style_name='galFiltered Style')''

5.3. Reference 197



py4cytoscape.style_mappings.set_node_border_opacity_mapping

set_node_border_opacity_mapping(table_column, table_column_values=None,opacities=None, mapping_type='c', de-fault_opacity=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Set opacity for node border only.

Parameters



• opacities (list) – int values between 0 and 255; 0 is invisible


• default_opacity (int) – Opacity value to set as default for all unmapped values






Raises



Examples

>>> set_node_border_opacity_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], opacities=[50, 100], style_name='galFiltered Style')''>>> set_node_border_opacity_mapping('Degree', table_column_values=['1', '2'],→˓opacities=[50, 100], mapping_type='d', style_name='galFiltered Style')''>>> set_node_border_opacity_mapping('PassthruCol', mapping_type='p', default_→˓opacity=225, style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_border_width_mapping

set_node_border_width_mapping(table_column, table_column_values=None, widths=None, map-ping_type='c', default_width=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to widths to set the node border width.

Parameters



• widths (list) – List of width values to map to table_column_values


• default_width (int) – Width value to set as default for all unmapped values






Raises



Examples

>>> set_node_border_width_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], widths=[5, 10], style_name='galFiltered Style')''>>> set_node_border_width_mapping('Degree', table_column_values=['1', '2'],→˓widths=[5, 10], mapping_type='d', style_name='galFiltered Style')''>>> set_node_border_width_mapping('PassthruCol', mapping_type='p', default_→˓width=3, style_name='galFiltered Style')''

5.3. Reference 199



py4cytoscape.style_mappings.set_node_color_mapping

set_node_color_mapping(table_column, table_column_values=None, colors=None, map-ping_type='c', default_color=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to colors to set the node fill color.

Parameters



• colors (list) – list of hex colors to map to table_column_values








Raises



Examples

>>> set_node_color_mapping('AverageShortestPathLength', [1.0, 16.36], ['#FBE723',→˓'#440256'], style_name='galFiltered Style')''>>> set_node_color_mapping('Degree', ['1', '2'], ['#FFFF00', '#00FF00'], 'd',→˓style_name='galFiltered Style')''>>> set_node_color_mapping('ColorCol', mapping_type='p', default_color='#654321',→˓style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_combo_opacity_mapping

set_node_combo_opacity_mapping(table_column, table_column_values=None, opacities=None,mapping_type='c', default_opacity=None, style_name='default',network=None, base_url='http://localhost:1234/v1')

Set opacity for node fill, border and label all together.

Parameters











Raises



Examples

>>> set_node_combo_opacity_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], opacities=[50, 100], style_name='galFiltered Style')''>>> set_node_combo_opacity_mapping('Degree', table_column_values=['1', '2'],→˓opacities=[50, 100], mapping_type='d', style_name='galFiltered Style')''>>> set_node_combo_opacity_mapping('PassthruCol', mapping_type='p', default_→˓opacity=225, style_name='galFiltered Style')''

5.3. Reference 201



py4cytoscape.style_mappings.set_node_fill_opacity_mapping

set_node_fill_opacity_mapping(table_column, table_column_values=None, opacities=None,mapping_type='c', default_opacity=None, style_name='default',network=None, base_url='http://localhost:1234/v1')

Set opacity for node fill only.

Parameters











Raises



Examples

>>> set_node_fill_opacity_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], opacities=[50, 100], style_name='galFiltered Style')''>>> set_node_fill_opacity_mapping('Degree', table_column_values=['1', '2'],→˓opacities=[50, 100], mapping_type='d', style_name='galFiltered Style')''>>> set_node_fill_opacity_mapping('PassthruCol', mapping_type='p', default_→˓opacity=225, style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_font_face_mapping

set_node_font_face_mapping(table_column, table_column_values=None, fonts=None, map-ping_type='d', default_font=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Sets font face for node labels.

Parameters



• fonts (list) – List of string specifications of font face, style and size, e.g.,[“SansSerif,plain,12”, “Dialog,plain,10”]

• mapping_type (str) – discrete or passthrough (d,p); default is discrete

• default_font (str) – String specification of font face, style and size, e.g.,“SansSerif,plain,12” or “Dialog,plain,10”






Raises



Examples

>>> set_node_font_face_mapping('Degree', table_column_values=['1', '2'], fonts=[→˓'Arial,plain,12', 'Arial Bold,bold,12'], mapping_type='d', style_name=→˓'galFiltered Style')''>>> set_node_font_face_mapping('PassthruCol', mapping_type='p', default_font=→˓'Arial,plain,12', style_name='galFiltered Style')''

5.3. Reference 203



py4cytoscape.style_mappings.set_node_font_size_mapping

set_node_font_size_mapping(table_column, table_column_values=None, sizes=None, map-ping_type='c', default_size=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to sizes to set the node size.

Parameters



• sizes (list) – List of size values to map to table_column_values


• default_size (int) – Size value to set as default






Raises



Examples

>>> set_node_font_size_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], sizes=[20, 80], style_name='galFiltered Style')''>>> set_node_font_size_mapping('Degree', table_column_values=['1', '2'],→˓sizes=[40, 90], mapping_type='d', style_name='galFiltered Style')''>>> set_node_font_size_mapping('PassthruCol', mapping_type='p', default_size=20,→˓style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_height_mapping

set_node_height_mapping(table_column, table_column_values=None, heights=None, map-ping_type='c', default_height=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to the node heights.

Parameters



• heights (list) – List of height values to map to table_column_values


• default_height (int) – Height value to set as default






Raises



Examples

>>> set_node_height_mapping('AverageShortestPathLength', table_column_values=[1.0,→˓ 16.36], sizes=[120, 180], style_name='galFiltered Style')''>>> set_node_height_mapping('Degree', table_column_values=['1', '2'], sizes=[140,→˓190], mapping_type='d', style_name='galFiltered Style')''>>> set_node_height_mapping('PassthruCol', mapping_type='p', default_size=120,→˓style_name='galFiltered Style')''

5.3. Reference 205



py4cytoscape.style_mappings.set_node_label_color_mapping

set_node_label_color_mapping(table_column, table_column_values=None, colors=None, map-ping_type='c', default_color=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to colors to set the node border color.

Parameters



• colors (list) – values between 0 and 255; 0 is invisible








Raises



Examples

>>> set_node_label_color_mapping('AverageShortestPathLength', [1.0, 16.36], ['→˓#FBE723', '#440256'], style_name='galFiltered Style')''>>> set_node_label_color_mapping('Degree', ['1', '2'], ['#FFFF00', '#00FF00'], 'd→˓', style_name='galFiltered Style')''>>> set_node_label_color_mapping('ColorCol', mapping_type='p', default_color='→˓#654321', style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_label_mapping

set_node_label_mapping(table_column, style_name='default', network=None,base_url='http://localhost:1234/v1')

Pass the values from a table column to display as node labels.

Parameters







Raises



Examples

>>> set_node_label_mapping('name', style_name='galFiltered Style')''>>> set_node_label_mapping('name')''

py4cytoscape.style_mappings.set_node_label_opacity_mapping

set_node_label_opacity_mapping(table_column, table_column_values=None, opacities=None,mapping_type='c', default_opacity=None, style_name='default',network=None, base_url='http://localhost:1234/v1')

Sets opacity for node label only.

Parameters







5.3. Reference 207







Raises



Examples

>>> set_node_label_opacity_mapping('AverageShortestPathLength', table_column_→˓values=[1.0, 16.36], opacities=[50, 100], style_name='galFiltered Style')''>>> set_node_label_opacity_mapping('Degree', table_column_values=['1', '2'],→˓opacities=[50, 100], mapping_type='d', style_name='galFiltered Style')''>>> set_node_label_opacity_mapping('PassthruCol', mapping_type='p', default_→˓opacity=225, style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_node_shape_mapping

set_node_shape_mapping(table_column, table_column_values=None, shapes=None, de-fault_shape=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to shapes to set the node shape.

Parameters



• shapes (list) – List of shapes to map to table_column_values. Seeget_node_shapes()

• default_shape (str) – Shape to set as default. See get_node_shapes()










Raises



Examples

>>> set_node_shape_mapping('Degree', table_column_values=['1', '2'], shapes=[→˓'TRIANGLE', 'OCTAGON'], default_shape='ELLIPSE', style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_node_size_mapping

set_node_size_mapping(table_column, table_column_values=None, sizes=None, map-ping_type='c', default_size=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to node sizes.

Parameters



• sizes (list) – List of sizes of nodes








Raises



5.3. Reference 209



Examples

>>> set_node_size_mapping('AverageShortestPathLength', table_column_values=[1.0,→˓16.36], sizes=[60, 100], style_name='galFiltered Style')''>>> set_node_size_mapping('Degree', table_column_values=['1', '2'], sizes=[60,→˓100], mapping_type='d', style_name='galFiltered Style')''>>> set_node_size_mapping('PassthruCol', mapping_type='p', default_opacity=40,→˓style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_node_tooltip_mapping

set_node_tooltip_mapping(table_column, style_name='default', network=None,base_url='http://localhost:1234/v1')

Pass the values from a table column to display as node tooltips.

Parameters







Raises



Examples

>>> set_node_tooltip_mapping('PassthruCol', style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_node_width_mapping

set_node_width_mapping(table_column, table_column_values=None, widths=None, map-ping_type='c', default_width=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to the node widths.

Parameters



• widths (list) – List of widths values to map to table_column_values


• default_width (int) – Width value to set as default






Raises



Examples

>>> set_node_width_mapping('AverageShortestPathLength', table_column_values=[1.0,→˓16.36], sizes=[120, 180], style_name='galFiltered Style')''>>> set_node_width_mapping('Degree', table_column_values=['1', '2'], sizes=[140,→˓190], mapping_type='d', style_name='galFiltered Style')''>>> set_node_width_mapping('PassthruCol', mapping_type='p', default_size=120,→˓style_name='galFiltered Style')''

5.3. Reference 211



Edge Style Mappings

set_edge_color_mapping(table_column[, . . . ])set_edge_font_face_mapping(table_column[,. . . ])

Sets font face for edge labels.

set_edge_font_size_mapping(table_column[,. . . ])

Map table column values to sizes to set the edge size.

set_edge_label_color_mapping(table_column[,. . . ])

Map table column values to colors to set the edge bordercolor.

set_edge_label_mapping(table_column[, . . . ]) Pass the values from a table column to display as edgelabels.

set_edge_label_opacity_mapping(table_column)Sets opacity for edge label only.set_edge_line_style_mapping(table_column[,. . . ])

Map table column values to styles to set the edge style.

set_edge_line_width_mapping(table_column[,. . . ])

Map table column values to widths to set the node bor-der width.

set_edge_opacity_mapping(table_column[,. . . ])

Map table column values to opacities to set the edgeopacity.

set_edge_source_arrow_color_mapping(table_column)Map table column values to colors to set the source ar-row color.

set_edge_source_arrow_mapping(table_column)Map table column values to shapes to set the source ar-row shape.

set_edge_source_arrow_shape_mapping(table_column)Map table column values to colors to set the source ar-row color.

set_edge_target_arrow_color_mapping(table_column)Map table column values to colors to set the target arrowcolor.

set_edge_target_arrow_maping(table_column[,. . . ])

Map table column values to shapes to set the target ar-row shape.

set_edge_target_arrow_shape_mapping(table_column)Map table column values to colors to set the target arrowcolor.

set_edge_tooltip_mapping(table_column[,. . . ])

Pass the values from a table column to display as edgetooltips.

py4cytoscape.style_mappings.set_edge_color_mapping

set_edge_color_mapping(table_column, table_column_values=None, colors=None, map-ping_type='c', default_color=None, style_name='default', network=None,base_url='http://localhost:1234/v1')

py4cytoscape.style_mappings.set_edge_font_face_mapping

set_edge_font_face_mapping(table_column, table_column_values=None, fonts=None, map-ping_type='d', default_font=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Sets font face for edge labels.

Parameters





• fonts (list) – List of string specifications of font face, style and size, e.g.,[“SansSerif,plain,12”, “Dialog,plain,10”]


• default_font (str) – String specification of font face, style and size, e.g.,“SansSerif,plain,12” or “Dialog,plain,10”






Raises



Examples

>>> set_edge_font_face_mapping('interaction', table_column_values=['pp', 'pd'],→˓fonts=['Arial,plain,12', 'Arial Bold,bold,12'], mapping_type='d', style_name=→˓'galFiltered Style')''>>> set_edge_font_face_mapping('PassthruCol', mapping_type='p', default_font=→˓'Arial,plain,12', style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_font_size_mapping

set_edge_font_size_mapping(table_column, table_column_values=None, sizes=None, map-ping_type='c', default_size=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to sizes to set the edge size.

Parameters



• sizes (list) – List of size values to map to table_column_values




5.3. Reference 213







Raises



Examples

>>> set_edge_font_size_mapping('EdgeBetweenness', table_column_values=[2.0, 20000.→˓0], sizes=[20, 80], style_name='galFiltered Style')''>>> set_edge_font_size_mapping('interaction', table_column_values=['pp', 'pd'],→˓sizes=[40, 90], mapping_type='d', style_name='galFiltered Style')''>>> set_edge_font_size_mapping('PassthruCol', mapping_type='p', default_size=20,→˓style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_label_color_mapping

set_edge_label_color_mapping(table_column, table_column_values=None, colors=None, map-ping_type='c', default_color=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to colors to set the edge border color.

Parameters




• mapping_type (str) – continuous, discrete or passthrough (c,d,p); default is continuou











Raises



Examples

>>> set_edge_label_color_mapping('EdgeBetweenness', [2.0, 20000.0], ['#FBE723', '→˓#440256'], style_name='galFiltered Style')''>>> set_edge_label_color_mapping('interaction', ['pp', 'pd'], ['#FFFF00', '#00FF00→˓'], 'd', style_name='galFiltered Style')''>>> set_edge_label_color_mapping('ColorCol', mapping_type='p', default_color='→˓#654321', style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_label_mapping

set_edge_label_mapping(table_column, style_name='default', network=None,base_url='http://localhost:1234/v1')

Pass the values from a table column to display as edge labels.

Parameters







Raises



5.3. Reference 215



Examples

>>> set_edge_label_mapping('name', style_name='galFiltered Style')''>>> set_edge_label_mapping('name')''

py4cytoscape.style_mappings.set_edge_label_opacity_mapping

set_edge_label_opacity_mapping(table_column, table_column_values=None, opacities=None,mapping_type='c', default_opacity=None, style_name='default',network=None, base_url='http://localhost:1234/v1')

Sets opacity for edge label only.

Parameters











Raises



Examples

>>> set_edge_label_opacity_mapping('EdgeBetweenness', [2.0, 20000.0],→˓opacities=[50, 100], style_name='galFiltered Style')''>>> set_edge_label_opacity_mapping('interaction', ['pp', 'pd'], opacities=[50,→˓100], mapping_type='d', style_name='galFiltered Style')''>>> set_edge_label_opacity_mapping('PassthruCol', mapping_type='p', default_→˓opacity=225, style_name='galFiltered Style')''




py4cytoscape.style_mappings.set_edge_line_style_mapping

set_edge_line_style_mapping(table_column, table_column_values=None, line_styles=None, de-fault_line_style='SOLID', style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to styles to set the edge style.

Parameters



• line_styles (list) – List of styles to map to table_column_values. Seeget_line_styles()

• default_line_style (str) – Style to set as default. See get_line_styles()






Raises



Examples

>>> set_edge_line_style_mapping('interaction', table_column_values=['pp','pd'],→˓shapes=['ZIGZAG', 'SINEWAVE'], default_shape='EQUAL_DASH', style_name=→˓'galFiltered Style')''

py4cytoscape.style_mappings.set_edge_line_width_mapping

set_edge_line_width_mapping(table_column, table_column_values=None, widths=None, map-ping_type='c', default_width=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to widths to set the node border width.

Parameters



5.3. Reference 217



• widths (list) – List of width values to map to table_column_values


• default_width (int) – Width value to set as default for all unmapped values






Raises



Examples

>>> set_edge_line_width_mapping('EdgeBetweenness', table_column_values=[2.0,→˓20000.0], widths=[5, 10], style_name='galFiltered Style')''>>> set_edge_line_width_mapping('interaction', table_column_values=['pp','pd'],→˓widths=[5, 10], mapping_type='d', style_name='galFiltered Style')''>>> set_edge_line_width_mapping('PassthruCol', mapping_type='p', default_width=3,→˓style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_opacity_mapping

set_edge_opacity_mapping(table_column, table_column_values=None, opacities=None, map-ping_type='c', default_opacity=None, style_name='default', net-work=None, base_url='http://localhost:1234/v1')

Map table column values to opacities to set the edge opacity.

Parameters














Raises



Examples

>>> set_edge_opacity_mapping('EdgeBetweenness', table_column_values=[2.0, 20000.→˓0], opacities=[50, 100], style_name='galFiltered Style')''>>> set_edge_opacity_mapping('interaction', table_column_values=['pp','pd'],→˓opacities=[50, 100], mapping_type='d', style_name='galFiltered Style')''>>> set_edge_opacity_mapping('PassthruCol', mapping_type='p', default_opacity=225,→˓ style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_source_arrow_color_mapping

set_edge_source_arrow_color_mapping(table_column, table_column_values=None, col-ors=None, mapping_type='c', default_color=None,style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to colors to set the source arrow color.

Parameters




• mapping_type (str) – continuous, discrete or passthrough (c,d,p); default is continuoue





5.3. Reference 219






Raises



Examples

>>> set_edge_source_arrow_color_mapping('EdgeBetweenness', [2.0, 20000.0], ['→˓#FBE723', '#440256'], style_name='galFiltered Style')''>>> set_edge_source_arrow_color_mapping('interaction', ['pp','pd'], ['#FFFF00', '→˓#00FF00'], 'd', style_name='galFiltered Style')''>>> set_edge_source_arrow_color_mapping('ColorCol', mapping_type='p', default_→˓color='#654321', style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_source_arrow_mapping

set_edge_source_arrow_mapping(table_column, table_column_values=None, shapes=None, de-fault_shape='ARROW', style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to shapes to set the source arrow shape.

Parameters



• shapes (list) – List of shapes to map to table_column_values. Seeget_arrow_shapes()

• default_shape (str) – Style to set as default. See get_arrow_shapes()






Raises






Examples

>>> set_edge_source_arrow_mapping('interaction', table_column_values=['pp','pd'],→˓shapes=['CIRCLE', 'ARROW'], default_shape='NONE', style_name='galFiltered Style→˓')''

py4cytoscape.style_mappings.set_edge_source_arrow_shape_mapping

set_edge_source_arrow_shape_mapping(table_column, table_column_values=None,shapes=None, default_shape=None,style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to colors to set the source arrow color.

Parameters



• shapes (list) – List of arrow shapes to map to table_column_values. Seeget_arrow_shapes()

• default_shape (str) – Shape to set as default. See get_arrow_shapes()






Raises



5.3. Reference 221



Examples

>>> set_edge_source_arrow_shape_mapping('interaction', table_column_values=['pp',→˓'pd'], shapes=['DIAMOND', 'CIRCLE'], style_name='galFiltered Style')''

Note: This is the same function as set_edge_source_arrow_mapping()

See also:

set_edge_source_arrow_mapping()

py4cytoscape.style_mappings.set_edge_target_arrow_color_mapping

set_edge_target_arrow_color_mapping(table_column, table_column_values=None, col-ors=None, mapping_type='c', default_color=None,style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to colors to set the target arrow color.

Parameters




• mapping_type (str) – continuous, discrete or passthrough (c,d,p); default is continuoue







Raises






Examples

>>> set_edge_target_arrow_color_mapping('EdgeBetweenness', [2.0, 20000.0], ['→˓#FBE723', '#440256'], style_name='galFiltered Style')''>>> set_edge_target_arrow_color_mapping('interaction', ['pp','pd'], ['#FFFF00', '→˓#00FF00'], 'd', style_name='galFiltered Style')''>>> set_edge_target_arrow_color_mapping('ColorCol', mapping_type='p', default_→˓color='#654321', style_name='galFiltered Style')''

py4cytoscape.style_mappings.set_edge_target_arrow_maping

set_edge_target_arrow_maping(table_column, table_column_values=None, shapes=None, de-fault_shape='ARROW', style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to shapes to set the target arrow shape.

Parameters



• shapes (list) – List of shapes to map to table_column_values. Seeget_arrow_shapes()

• default_shape (str) – Style to set as default. See get_arrow_shapes()






Raises



5.3. Reference 223



Examples

>>> set_edge_target_arrow_maping('interaction', table_column_values=['pp','pd'],→˓shapes=['CIRCLE', 'ARROW'], default_shape='NONE', style_name='galFiltered Style→˓')''

py4cytoscape.style_mappings.set_edge_target_arrow_shape_mapping

set_edge_target_arrow_shape_mapping(table_column, table_column_values=None,shapes=None, default_shape=None,style_name='default', network=None,base_url='http://localhost:1234/v1')

Map table column values to colors to set the target arrow color.

Parameters



• shapes (list) – List of arrow shapes to map to table_column_values. Seeget_arrow_shapes()

• default_shape (str) – Shape to set as default. See get_arrow_shapes()






Raises



Examples

>>> set_edge_source_arrow_target_mapping('interaction', table_column_values=['pp',→˓'pd'], shapes=['DIAMOND', 'CIRCLE'], style_name='galFiltered Style')''

Note: This is the same function as set_edge_target_arrow_mapping()

See also:




set_edge_target_arrow_mapping()

py4cytoscape.style_mappings.set_edge_tooltip_mapping

set_edge_tooltip_mapping(table_column, style_name='default', network=None,base_url='http://localhost:1234/v1')

Pass the values from a table column to display as edge tooltips.

Parameters







Raises



Examples

>>> set_edge_tooltip_mapping('PassthruCol', style_name='galFiltered Style')''

Style Values

Functions for retrieving current values for visual properties.

I. General functions for getting node, edge and network properties

II. Specific functions for getting particular node, edge and network properties

Node Style Values

get_node_color([node_names, network,base_url])

Retrieve the actual fill color of specified nodes.

get_node_height([node_names, network,base_url])

Retrieve the actual height of specified nodes.

get_node_position([node_names, network, . . . ]) Retrieve the actual x,y position of specified nodes.get_node_property([node_names, . . . ]) Get values for any node property of the specified nodes.


5.3. Reference 225



Table 45 – continued from previous pageget_node_size([node_names, network, base_url]) Retrieve the actual size of specified nodes.get_node_width([node_names, network,base_url])

Retrieve the actual width of specified nodes.

py4cytoscape.style_values.get_node_color

get_node_color(node_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual fill color of specified nodes.

Parameters

• node_names (list) – List of node names or node SUIDs. Default is None for all nodes.



Returns as a collection of {node-name: fill-color} for each node in node_names parameter

Return type dict

Raises

• CyError – if network name or node doesn’t exist


Examples

>>> get_node_color()>>> {'YOR215C': '#FFFFEC', 'YBL026W': '#FCFDFE', 'YOL149W': '#FFFFE3', ...}>>> get_node_color(['YOR215C', 'YBL026W', 'YOL149W'])>>> {'YOR215C': '#FFFFEC', 'YBL026W': '#FCFDFE', 'YOL149W': '#FFFFE3'}>>> get_node_color([395406, 395407, 395404])>>> {395406: '#FFFFEC', 395407: '#FCFDFE', 395404: '#FFFFE3'}>>> get_node_color(node_names='YOR215C', network='galFiltered.sif')>>> {'YYOR215C': '#FFFFEC'}

py4cytoscape.style_values.get_node_height

get_node_height(node_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual height of specified nodes.

Parameters







Returns as a collection of {node-name: height} for each node in node_names parameter

Return type dict

Raises



Examples

>>> get_node_height()>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0, ...}>>> get_node_height(['YOR215C', 'YBL026W', 'YOL149W'])>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0}>>> get_node_height([395406, 395407, 395404])>>> {395406: 50.0, 395407: 50.0, 395404: 50.0}>>> get_node_height(node_names='YOR215C', network='galFiltered.sif')>>> {'YYOR215C': 46.470588235294116}

py4cytoscape.style_values.get_node_position

get_node_position(node_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual x,y position of specified nodes.

Parameters




Returns with index as node_names values and columns x and y containing coordinates

Return type dataframe

Raises



5.3. Reference 227




Examples

>>> get_node_position()>>> x y>>> YIL052C 2628.866343678256 1180.9601936051579>>> YDL215C 1723.7108261001308 2230.935871095392>>> YLR432W 1660.9524948013027 2387.6488532731264>>> ...>>> get_node_position(['YDR429C', 'YMR005W', 'YDR142C'])>>> x y>>> YDR429C 2628.866343678256 1180.9601936051579>>> YMR005W 1723.7108261001308 2230.935871095392>>> YDR142C 1660.9524948013027 2387.6488532731264>>> get_node_position([432646, 432647, 432644])>>> x y>>> 432646 2628.866343678256 1180.9601936051579>>> 432647 1723.7108261001308 2230.935871095392>>> 432644 1660.9524948013027 2387.6488532731264>>> get_node_position(node_names='YER112W', network='galFiltered.sif')>>> x y>>> YER112W 2151.8481399429043 2326.677814454767

py4cytoscape.style_values.get_node_property

get_node_property(node_names=None, visual_property=None, network=None,base_url='http://localhost:1234/v1')

Get values for any node property of the specified nodes.

Parameters


• visual_property (str) – Name of a visual property. Seeget_visual_property_names



Returns as a collection of {node-name: prop_value} for each node in node_names parameter

Return type dict

Raises

• CyError – if network name, node name or property name doesn’t exist





Examples

>>> get_node_property(visual_property='NODE_LABEL')>>> {'YIL070C': 'MAM33', 'YHR198C': 'YHR198C', ...}>>> get_node_property(visual_property='NODE_LABEL', node_names=['YIL070C',→˓'YHR198C'])>>> {'YIL070C': 'MAM33', 'YHR198C': 'YHR198C'}>>> get_node_property(visual_property='NODE_LABEL', node_names=[391173, 391172,→˓391175])>>> {391173: 'RPL11B', 391172: 'SXM1', 391175: 'MPT1'}>>> get_node_property(visual_property='NODE_LABEL', node_names='YER112W', network=→˓'galFiltered.sif')>>> {'YER112W': 'LSM4'}

py4cytoscape.style_values.get_node_size

get_node_size(node_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual size of specified nodes.

Parameters




Returns as a collection of {node-name: size} for each node in node_names parameter

Return type dict

Raises



Examples

>>> get_node_size()>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0, ...}>>> get_node_size(['YOR215C', 'YBL026W', 'YOL149W'])>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0}>>> get_node_size([395406, 395407, 395404])>>> {395406: 50.0, 395407: 50.0, 395404: 50.0}>>> get_node_size(node_names='YOR215C', network='galFiltered.sif')>>> {'YYOR215C': 50.0}

5.3. Reference 229



py4cytoscape.style_values.get_node_width

get_node_width(node_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual width of specified nodes.

Parameters




Returns as a collection of {node-name: width} for each node in node_names parameter

Return type dict

Raises



Examples

>>> get_node_width()>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0, ...}>>> get_node_width(['YOR215C', 'YBL026W', 'YOL149W'])>>> {'YOR215C': 50.0, 'YBL026W': 50.0, 'YOL149W': 50.0}>>> get_node_width([395406, 395407, 395404])>>> {395406: 50.0, 395407: 50.0, 395404: 50.0}>>> get_node_width(node_names='YOR215C', network='galFiltered.sif')>>> {'YYOR215C': 46.470588235294116}

Edge Style Values

get_edge_color([edge_names, network,base_url])

Retrieve the actual line color of specified edges.

get_edge_line_style([edge_names, network,. . . ])

Retrieve the actual line style of specified edges.

get_edge_line_width([edge_names, network,. . . ])

Retrieve the actual line width of specified edge.

get_edge_property([edge_names, . . . ]) Get values for any edge property of the specified edges.get_edge_target_arrow_shape([edge_names,. . . ])

Retrieve the actual target arrow shape of specifiededges.




py4cytoscape.style_values.get_edge_color

get_edge_color(edge_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual line color of specified edges.

Parameters

• edge_names (list) – List of edge names or edge SUIDs. Default is None for all edges.



Returns as a collection of {edge-name: line-color} for each edge in edge_names parameter

Return type dict

Raises

• CyError – if network name or edge doesn’t exist


Examples

>>> get_edge_color()>>> {'YMR117C (pp) YCL032W': '#808080', 'YMR255W (pp) YGL122C': '#808080',→˓'YNL214W (pp) YGL153W': '#808080', ...}>>> get_edge_color(['YHR084W (pd) YFL026W', 'YHR084W (pd) YDR461W', 'YMR255W (pp)→˓YGL122C'])>>> {'YHR084W (pd) YFL026W': '#808080', 'YHR084W (pd) YDR461W': '#808080',→˓'YMR255W (pp) YGL122C': '#808080'}>>> get_edge_color([421382, 421383, 421380])>>> {421382: '#808080', 421383: '#808080', 421380: '#808080'}>>> get_edge_color(edge_names='YOR355W (pp) YNL091W', network='galFiltered.sif')>>> {'YOR355W (pp) YNL091W': '#808080'}

py4cytoscape.style_values.get_edge_line_style

get_edge_line_style(edge_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual line style of specified edges.

Parameters




Returns as a collection of {edge-name: line-style} for each edge in edge_names parameter

Return type dict

5.3. Reference 231




Raises



Examples

>>> get_edge_line_style()>>> {'YMR117C (pp) YCL032W': 'SOLID', 'YMR255W (pp) YGL122C': 'SOLID', 'YNL214W→˓(pp) YGL153W': 'SOLID', ...}>>> get_edge_line_style(['YHR084W (pd) YFL026W', 'YHR084W (pd) YDR461W', 'YMR255W→˓(pp) YGL122C'])>>> {'YHR084W (pd) YFL026W': 'SOLID', 'YHR084W (pd) YDR461W': 'SOLID', 'YMR255W→˓(pp) YGL122C': 'SOLID'}>>> get_edge_line_style([421382, 421383, 421380])>>> {421382: 'SOLID', 421383: 'SOLID', 421380: 'SOLID'}>>> get_edge_line_style(edge_names='YOR355W (pp) YNL091W', network='galFiltered.→˓sif')>>> {'YOR355W (pp) YNL091W': 'SOLID'}

py4cytoscape.style_values.get_edge_line_width

get_edge_line_width(edge_names=None, network=None, base_url='http://localhost:1234/v1')Retrieve the actual line width of specified edge.

Parameters




Returns as a collection of {edge-name: width} for each edge in edge_names parameter

Return type dict

Raises






Examples

>>> get_edge_line_width()>>> {'YLR197W (pp) YOR310C': 2.0, 'YIL074C (pp) YNL311C': 2.0, ...}>>> get_edge_line_width(['YHR084W (pd) YFL026W', 'YHR084W (pd) YDR461W', 'YMR255W→˓(pp) YGL122C'])>>> {'YHR084W (pd) YFL026W': 2.0, 'YHR084W (pd) YDR461W': 2.0, 'YMR255W (pp)→˓YGL122C': 2.0}>>> get_edge_line_width([421382, 421383, 421380])>>> {421382: 2.0, 421383: 2.0, 421380: 2.0}>>> get_edge_line_width(edge_names='YOR355W (pp) YNL091W', network='galFiltered.→˓sif')>>> {'YOR355W (pp) YNL091W': 2.0}

py4cytoscape.style_values.get_edge_property

get_edge_property(edge_names=None, visual_property=None, network=None,base_url='http://localhost:1234/v1')

Get values for any edge property of the specified edges.

This method retrieves the actual property of the node, given the current visual style, factoring together anydefault, mapping and bypass setting.

Parameters

• edge_names (list) – List of edge names or node SUIDs. Default is None for all edges.




Returns as a collection of {edge-name: prop_value} for each edge in edge_names parameter

Return type dict

Raises

• CyError – if network name, edge name or property name doesn’t exist


Examples

>>> get_edge_property(visual_property='EDGE_LABEL')>>> {'YJR022W (pp) YNL050C': 'pp', 'YKR026C (pp) YGL122C': 'pp', ...}>>> get_edge_property(visual_property='EDGE_LABEL', edge_names=['YCL067C (pd)→˓YIL015W', 'YCR084C (pp) YCL067C'])>>> {'YCL067C (pd) YIL015W': 'pd', 'YCR084C (pp) YCL067C': 'pp'}>>> get_edge_property(visual_property='EDGE_LABEL', edge_names=[393222, 393223])>>> {393222: 'pd', 393223: 'pp'}

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5.3. Reference 233



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>>> get_edge_property(visual_property='EDGE_LABEL', edge_names='YDR277C (pp)→˓YJR022W', network='galFiltered.sif')>>> {'YDR277C (pp) YJR022W': 'pp'}

py4cytoscape.style_values.get_edge_target_arrow_shape

get_edge_target_arrow_shape(edge_names=None, network=None,base_url='http://localhost:1234/v1')

Retrieve the actual target arrow shape of specified edges.

Parameters




Returns as a collection of {edge-name: arrow-shape} for each edge in edge_names parameter

Return type dict

Raises



Examples

>>> get_edge_target_arrow_shape()>>> {'YMR117C (pp) YCL032W': 'NONE', 'YMR255W (pp) YGL122C': 'NONE', 'YNL214W→˓(pp) YGL153W': 'NONE', ...}>>> get_edge_target_arrow_shape(['YHR084W (pd) YFL026W', 'YHR084W (pd) YDR461W',→˓'YMR255W (pp) YGL122C'])>>> {'YHR084W (pd) YFL026W': 'NONE', 'YHR084W (pd) YDR461W': 'NONE', 'YMR255W→˓(pp) YGL122C': 'NONE'}>>> get_edge_target_arrow_shape([421382, 421383, 421380])>>> {421382: 'NONE', 421383: 'NONE', 421380: 'NONE'}>>> get_edge_target_arrow_shape(edge_names='YOR355W (pp) YNL091W', network=→˓'galFiltered.sif')>>> {'YOR355W (pp) YNL091W': 'NONE'}




Network Style Values

get_network_center([network, base_url]) Retrieve the center of specified network.get_network_property(visual_property[, . . . ]) Get values for any network property.get_network_zoom([network, base_url]) Retrieve the scale factor of specified network.

py4cytoscape.style_values.get_network_center

get_network_center(network=None, base_url='http://localhost:1234/v1')Retrieve the center of specified network.

Parameters



Returns as {x: x-coord, y: y-coord} for center of network

Return type dict

Raises



Examples

>>> get_network_center()>>> {'x': 2628.866343678256, 'y': 1180.9601936051579}>>> get_network_center(network='galFiltered.sif')>>> {'x': 2628.866343678256, 'y': 1180.9601936051579}

py4cytoscape.style_values.get_network_property

get_network_property(visual_property, network=None, base_url='http://localhost:1234/v1')Get values for any network property.

This method retrieves the actual property of the network, given the current visual style, factoring together anydefault, mapping and bypass setting.

Parameters



5.3. Reference 235




Returns value of visual property

Return type float

Raises

• CyError – if network name or property name doesn’t exist


Examples

>>> get_network_property('NETWORK_SCALE_FACTOR')>>> 0.6299925248514752>>> get_network_property(visual_property='NETWORK_SCALE_FACTOR', network=→˓'galFiltered.sif')>>> 0.6299925248514752

py4cytoscape.style_values.get_network_zoom

get_network_zoom(network=None, base_url='http://localhost:1234/v1')Retrieve the scale factor of specified network.

Parameters



Returns for zoom factor

Return type float

Raises







Examples

>>> get_network_zoom()>>> 0.6299925248514752>>> get_network_zoom(network='galFiltered.sif')>>> 0.6299925248514752

5.3.13 Tables

Functions for managing TABLE columns and table column functions, like map and rename, as well as loading andextracting table data in Cytoscape.

Column Manipulation

delete_table_column(column[, table, . . . ]) Delete a column from node, edge or network tables.get_table_column_names([table, namespace,. . . ])

Retrieve the names of all columns in a table.

get_table_column_types([table, namespace,. . . ])

Retrieve the types of all columns in a table.

get_table_columns([table, columns, . . . ]) Retrieve one or more columns of data from node, edgeor network tables.

rename_table_column(column, new_name[, . . . ]) Set a new name for a column.

py4cytoscape.tables.delete_table_column

delete_table_column(column, table='node', namespace='default', network=None,base_url='http://localhost:1234/v1')

Delete a column from node, edge or network tables.

Parameters

• column (str) – Name of the column to delete

• table (str) – Name of table, e.g., node (default), edge, network

• namespace (str) – Namespace of table. Default is “default”.



Returns

’‘

Return type str

Note: No error is returned if the column doesn’t exist in the table

Raises

5.3. Reference 237



• HTTPError – if table or namespace doesn’t exist in network



Examples

>>> delete_table_column('BetweennessCentrality')''>>> delete_table_column('EdgeBetweenness', table='edge')''>>> delete_table_column('BetweennessCentrality', network='My Network')''

py4cytoscape.tables.get_table_column_names

get_table_column_names(table='node', namespace='default', network=None,base_url='http://localhost:1234/v1')

Retrieve the names of all columns in a table.

Parameters

• table (str) – Name of table, e.g., node, edge, network; default is “node”




Returns list of column names

Return type list

Raises

• HTTPError – if table or namespace or table doesn’t exist in network



Examples

>>> get_table_column_names()['SUID', 'shared name', 'name', 'selected', 'AverageShortestPathLength', ... ]>>> get_table_column_names('edge')['SUID', 'shared name', 'shared interaction', 'name', 'selected', 'interaction',→˓'EdgeBetweenness']>>> get_table_column_names('network', network='My Network')['SUID', 'shared name', 'name', 'selected', '__Annotations', 'publication',→˓'Dataset Name', 'Dataset URL']




py4cytoscape.tables.get_table_column_types

get_table_column_types(table='node', namespace='default', network=None,base_url='http://localhost:1234/v1')

Retrieve the types of all columns in a table.

Parameters

• table (str) – Name of table, e.g., node, edge, network; default is “node”




Returns where the column name is the key and the data type is the value

Return type dict

Raises




Examples

>>> get_table_column_types(){'SUID': 'Long', 'shared name': 'String', 'name': 'String', 'selected': 'Boolean',→˓ 'AverageShortestPathLength': 'Double', ...}>>> get_table_column_types('edge'){'SUID': 'Long', 'shared name': 'String', 'shared interaction': 'String', 'name':→˓'String', ... }>>> get_table_column_types('network', network='My Network'){'SUID': 'Long', 'shared name': 'String', 'name': 'String', 'selected': 'Boolean',→˓ '__Annotations': 'List', ...}

py4cytoscape.tables.get_table_columns

get_table_columns(table='node', columns=None, namespace='default', network=None,base_url='http://localhost:1234/v1')

Retrieve one or more columns of data from node, edge or network tables.

The ‘SUID’ column is always retrieved along with specified columns. The ‘SUID’ values are used as index inthe returned dataframe.

Parameters


• columns (str or list or None) – Names of columns to retrieve values from as listobject or comma-separated list; default is all columns

5.3. Reference 239






Returns requested columns (including SUID), and rows for each node/edge or network.


Raises

• HTTPError – if table or namespace doesn’t exist in network



Examples

>>> get_table_columns()SUID shared name name ... gal4RGsig gal80Rsig isExcludedFromPaths

3072 3072 YDL081C YDL081C ... 0.048133 5.9631e-06 False3073 3073 YGL166W YGL166W ... 0.0012181 0.032147 False...>>> get_table_columns(columns='name')

SUID shared name name ... gal4RGsig gal80Rsig isExcludedFromPaths3072 3072 YDL081C YDL081C ... 0.048133 5.9631e-06 False3073 3073 YGL166W YGL166W ... 0.0012181 0.032147 False...>>> get_table_columns(columns=['gal1RGexp', 'Eccentricity', 'Stress'])

gal1RGexp Eccentricity Stress4608 -0.262 17 04609 -0.704 17 2092...>>> get_table_columns(columns='Stress, NumberOfDirectedEdges')

Stress NumberOfDirectedEdges4608 0 14609 2092 2...>>> get_table_columns(columns='Stress, bogus')

Stress bogus4608 0 NaN4609 2092 NaN...

Note: For requested columns not present in the table, the column is still returned but is full of nan values.




py4cytoscape.tables.rename_table_column

rename_table_column(column, new_name, table='node', namespace='default', network=None,base_url='http://localhost:1234/v1')

Set a new name for a column.

Parameters

• column (str) – Name of the column to rename

• new_name (str) – New name for the specified column

• table (str) – name of Cytoscape table to load data into, e.g., node, edge or network;default is “node”




Returns

’‘

Return type str

Raises

• HTTPError – if table or namespace or table doesn’t exist in network, or if column doesn’texist in table, or new_name already exists

• CyError – if network name or SUID doesn’t exist, or if mapping parameter is invalid


Examples

>>> rename_table_column('AverageShortestPathLength', 'xAveragex')''>>> rename_table_column('AverageShortestPathLength', 'xAveragex', table='edge',→˓namespace='default', network='My Network')''

Column Mapping

map_table_column(column, species, map_from,. . . )

Map Table Column.

5.3. Reference 241



py4cytoscape.tables.map_table_column

map_table_column(column, species, map_from, map_to, force_single=True, table='node', names-pace='default', network=None, base_url='http://localhost:1234/v1')

Map Table Column.

Perform identifier mapping using an existing column of supported identifiers to populate a new column withidentifiers mapped to the originals.

Supported species: Human, Mouse, Rat, Frog, Zebrafish, Fruit fly, Mosquito, Worm, Arabidopsis thaliana,Yeast, E. coli, Tuberculosis. Supported identifier types (depending on species): Ensembl, Entrez Gene, Uniprot-TrEMBL, miRBase, UniGene, HGNC (symbols), MGI, RGD, SGD, ZFIN, FlyBase, WormBase, TAIR.

Parameters

• column (str) – Name of column containing identifiers of type specified by map.from

• species (str) – Common name for species associated with identifiers, e.g., Human. Seedetails.

• map_from (str) – Type of identifier found in specified column. See details.

• map.to (str) – Type of identifier to populate in new column. See details.

• force.single (bool) – Whether to return only first result in cases of one-to-manymappings; otherwise the new column will hold lists of identifiers. Default is TRUE.





Returns contains map_from and map_to columns.


Warning: If map_to is not unique, it will be suffixed with an incrementing number in parentheses, e.g.,if mapIdentifiers is repeated on the same network. However, the original map_to column will be returnedregardless.

Raises


• CyError – if network name or SUID doesn’t exist, or if mapping parameter is invalid





Examples

>>> map_table_column('name','Yeast','Ensembl','SGD')name SGD

17920 YER145C S00000094717921 YMR058W S00000466217922 YJL190C S000003726...

Data Values

get_table_value(table, row_name, column[, . . . ]) Retrieve the value from a specific row and column fromnode, edge or network tables.

load_table_data(data[, data_key_column, . . . ]) Loads data into Cytoscape tables keyed by row.

py4cytoscape.tables.get_table_value

get_table_value(table, row_name, column, namespace='default', network=None,base_url='http://localhost:1234/v1')

Retrieve the value from a specific row and column from node, edge or network tables.

Parameters


• row_name (str) – Node, edge or network name, i.e., the value in the “name” column

• column (str) – Name of column to retrieve values from




Returns the value of the table cell, cast to float, int, bool or str depending on column type

Return type obj

Raises

• HTTPError – if table or namespace doesn’t exist in network or if cell contains a numerictype but no number



5.3. Reference 243



Examples

>>> get_table_value('node', 'YDL194W', 'COMMON')'SNF3'>>> get_table_value('edge', 'YLR197W (pp) YOR310C', 'EdgeBetweenness', network=→˓'My Network')2.0>>> get_table_value('node', 'YDL194W', 'IsSingleNode')False

py4cytoscape.tables.load_table_data

load_table_data(data, data_key_column='row.names', table='node', table_key_column='name', names-pace='default', network=None, base_url='http://localhost:1234/v1')

Loads data into Cytoscape tables keyed by row.

This function loads data into Cytoscape node/edge/network tables provided a common key, e.g., name.Data.frame column names will be used to set Cytoscape table column names. Numeric values will be storedas Doubles in Cytoscape tables. Integer values will be stored as Integers. Character or mixed values will bestored as Strings. Logical values will be stored as Boolean. Lists are stored as Lists by CyREST v3.9+. Existingcolumns with the same names will keep original type but values will be overwritten.

Parameters

• data (dataframe) – each row is a node and columns contain node attributes

• data_key_column (str) – name of data.frame column to use as key; ‘ default is“row.names”





Returns ‘Success: Data loaded in <table name> table’ or ‘Failed to load data: <reason>’

Return type str

Raises







Examples

>>> data = df.DataFrame(data={'id':['New1','New2','New3'], 'newcol':[1,2,3]})>>> load_table_data(data, data_key_column='id', table='node', table_key_column=→˓'name')'Failed to load data: Provided key columns do not contain any matches'>>> data = df.DataFrame(data={'id':['YDL194W','YDR277C','YBR043C'], 'newcol':[1,2,→˓3]})>>> load_table_data(data, data_key_column='id', table='node', table_key_column=→˓'name', network='galfiltered.sif')'Success: Data loaded in defaultnode table'

5.3.14 Tools

Functions related to TOOLS found in the Tools Menu in Cytoscape.

Browser Control

cybrowser_close([id, base_url]) Cybrowser Close.cybrowser_dialog([id, text, title, url, . . . ]) Launch Cytoscape’s internal web browser in a separate

windowcybrowser_hide([id, base_url]) Cybrowser Hide.cybrowser_list([base_url]) Cybrowser List.cybrowser_send([id, script, base_url]) Cybrowser Send.cybrowser_show([id, text, title, url, base_url]) Cybrowser Show.cybrowser_version([base_url]) Display the version of the CyBrowser app.

py4cytoscape.tools.cybrowser_close

cybrowser_close(id=None, base_url='http://localhost:1234/v1')Cybrowser Close.

Close an internal web browser and remove all content. Provide an id for the browser you want to close.

Parameters

• id (str) – The identifier for the browser window to close


Returns {}

Return type dict


5.3. Reference 245



Examples

>>> cybrowser_close('CyGame'){}

py4cytoscape.tools.cybrowser_dialog

cybrowser_dialog(id=None, text=None, title=None, url=None, base_url='http://localhost:1234/v1')Launch Cytoscape’s internal web browser in a separate window

Provide an id for the window if you want subsequent control of the window e.g., via cybrowser hide.

Parameters

• id (str) – The identifier for the new browser window

• text (str) – HTML text to initially load into the browser

• title (str) – Text to be shown in the title bar of the browser window

• url (str) – The URL the browser should load


Returns {‘id’: id} where id is the one provided as a parameter to this function

Return type dict


Examples

>>> cybrowser_dialog(id='Test Window', title='Hello Africa', text='<HTML><HEAD>→˓<TITLE>Hello</TITLE></HEAD><BODY>Hello, world!</BODY></HTML>'){'id': 'Test Window'}>>> cybrowser_dialog(id='CytoWindow', title='Cytoscape Home Page', url='http://→˓www.cytoscape.org'){'id': 'CytoWindow'}

See also:

cybrowser_show(), cybrowser_hide()

py4cytoscape.tools.cybrowser_hide

cybrowser_hide(id=None, base_url='http://localhost:1234/v1')Cybrowser Hide.

Hide an existing browser, whether it’s in the Results panel or a separate window.

Parameters

• id (str) – The identifier for the browser window to hide





Returns {}

Return type dict


Examples

>>> cybrowser_hide('CyGame'){}

See also:

cybrowser_show(), cybrowser_dialog()

py4cytoscape.tools.cybrowser_list

cybrowser_list(base_url='http://localhost:1234/v1')Cybrowser List.

List all browsers that are currently open, whether as a dialog or in the results panel.


Returns [{‘id’: id, ‘title’: title, ‘url’: current url}]

Return type list


Examples

>>> cybrowser_list()[{'id': 'CytoManual ID', 'title': 'CytoManual Page', 'url': 'http://manual.→˓cytoscape.org/en/stable/'}, {'id': ...} ...]

Note: In the return value, there is a dict for each browser window, and the id and title were provided in thecybrowser_show() call, and the url is for the page currently loaded in the browser window

5.3. Reference 247




py4cytoscape.tools.cybrowser_send

cybrowser_send(id=None, script='', base_url='http://localhost:1234/v1')Cybrowser Send.

Send the text to the browser indicated by the id and return the response, if any. Note that the JSON result fieldcould either be a bare string or JSON formatted text.

Parameters


• script (str) – Note that only string results are returned.


Returns {‘browserId’: id, ‘result’: result}

Return type dict

Raises

• CyError – if the browser could not execute the command


Examples

>>> cybrowser_send(id='Test Window', script='navigator.userAgent'){'browserId': 'Test Window', 'result': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64)→˓AppleWebKit/608.1 (KHTML, like Gecko) JavaFX/13 Safari/608.1 CyBrowser/1.2.0'}>>> cybrowser_send(id='CytoWindow', script="window.location='http://google.com'"){'browserId': 'CytoWindow', 'result': 'http://google.com'}

Note: In the return result, id is the one provided as a parameter to this function and result is the stringreturned as a result of executing the script

See also:

cybrowser_show(), cybrowser_hide(), cybrowser_dialog()

py4cytoscape.tools.cybrowser_show

cybrowser_show(id=None, text=None, title=None, url=None, base_url='http://localhost:1234/v1')Cybrowser Show.

Launch Cytoscape’s internal web browser in a pane in the Result Panel. Provide an id for the window if youwant subsequent control of the window via cybrowser hide.

Parameters


• text (str) – HTML text to initially load into the browser

• title (str) – Text to be shown in the title bar of the browser window




• url (str) – The URL the browser should load


Returns {‘id’: id} where id is the one provided as a parameter to this function

Return type dict


Examples

>>> cybrowser_show(id='Test Window', title='Hello Africa', text='<HTML><HEAD>→˓<TITLE>Hello</TITLE></HEAD><BODY>Hello, world!</BODY></HTML>'){'id': 'Test Window'}>>> cybrowser_show(id='CytoWindow', title='Cytoscape Home Page', url='http://www.→˓cytoscape.org'){'id': 'CytoWindow'}

See also:

cybrowser_dialog(), cybrowser_hide()

py4cytoscape.tools.cybrowser_version

cybrowser_version(base_url='http://localhost:1234/v1')Display the version of the CyBrowser app.


Returns {‘version’: app version} where app version is the CyBrowser app version

Return type dict


Examples

>>> cybrowser_version(){'version': '1.2.0'}

5.3. Reference 249




Diffusion

diffusion_advanced([heat_column_name, time,. . . ])

Diffusion Advanced.

diffusion_basic([base_url]) Diffusion Basic.

py4cytoscape.tools.diffusion_advanced

diffusion_advanced(heat_column_name=None, time=None, base_url='http://localhost:1234/v1')Diffusion Advanced.

Diffusion will send the selected network view and its selected nodes to a web-based REST service to calculatenetwork propagation. Results are returned and represented by columns in the node table. Advanced operationsupports parameters.

Columns are created for each execution of Diffusion and their names are returned in the response. Thenodes you would like to use as input should be selected. This will be used to generate the contents of thediffusion_input column, which represents the query vector and corresponds to h in the diffusion equa-tion.

Parameters

• heat_column_name (str) – A node column name intended to override the default tablecolumn diffusion_input. This represents the query vector and corresponds to h in thediffusion equation.

• time (str) – The extent of spread over the network. This corresponds to t in the diffusionequation.


Returns {‘heatColumn’: ‘diffusion_output_heat’, ‘rankColumn’: ‘diffusion_output_rank’} whereheatColumn is the name of the node table column containing each node’s calculated heat andrankColumn is the name of the node table column containing the node’s (0-based) rank

Return type dict

Raises

• CyError – if an invalid parameter is passed


Examples

>>> diffusion_advanced(heat_column_name='diffusion_output_heat', time=0.1){'heatColumn': 'diffusion_output_1_heat', 'rankColumn': 'diffusion_output_1_rank'}




py4cytoscape.tools.diffusion_basic

diffusion_basic(base_url='http://localhost:1234/v1')Diffusion Basic.

Diffusion will send the selected network view and its selected nodes to a web-based REST service to calculatenetwork propagation. Results are returned and represented by columns in the node table.

Columns are created for each execution of Diffusion and their names are returned in the response. Thenodes you would like to use as input should be selected. This will be used to generate the contents of thediffusion_input column, which represents the query vector and corresponds to h in the diffusion equa-tion.


Returns {‘heatColumn’: ‘diffusion_output_heat’, ‘rankColumn’: ‘diffusion_output_rank’} whereheatColumn is the name of the node table column containing each node’s calculated heat andrankColumn is the name of the node table column containing the node’s (0-based) rank

Return type dict


Examples

>>> diffusion_basic(){'heatColumn': 'diffusion_output_heat', 'rankColumn': 'diffusion_output_rank'}

5.3.15 User Interface

Functions affecting the USER INTERFACE, such as panel management.

Panels

dock_panel(panel_name[, base_url]) Dock a panel back into the UI of Cytoscape.float_panel(panel_name[, base_url]) Pop out a panel from the UI of Cytoscape.hide_all_panels([base_url]) Hide control, table, tool and results panels.hide_panel(panel_name[, base_url]) Hide a panel in the UI of Cytoscape.

py4cytoscape.user_interface.dock_panel

dock_panel(panel_name, base_url='http://localhost:1234/v1')Dock a panel back into the UI of Cytoscape.

Parameters

• panel_name (str) – Name of the panel. Multiple ways of referencing panels issupported: (WEST == control panel, control, c), (SOUTH == table panel, table, ta),(SOUTH_WEST == tool panel, tool, to), (EAST == results panel, results, r)

5.3. Reference 251




Returns

’‘

Return type str

Raises

• CyError – if panel name is not recognized


Examples

>>> dock_panel('control panel')''>>> dock_panel('WEST')''

py4cytoscape.user_interface.float_panel

float_panel(panel_name, base_url='http://localhost:1234/v1')Pop out a panel from the UI of Cytoscape.

Other panels will expand into the space.

Parameters



Returns

’‘

Return type str

Raises







Examples

>>> float_panel('control panel')''>>> float_panel('WEST')''

py4cytoscape.user_interface.hide_all_panels

hide_all_panels(base_url='http://localhost:1234/v1')Hide control, table, tool and results panels.

Parameters



Returns None

Raises



Examples

>>> hide_all_panels()''>>> hide_all_panels()''

py4cytoscape.user_interface.hide_panel

hide_panel(panel_name, base_url='http://localhost:1234/v1')Hide a panel in the UI of Cytoscape.

Other panels will expand into the space.

Parameters



5.3. Reference 253




Returns

’‘

Return type str

Raises



Examples

>>> hide_panel('control panel')''>>> hide_panel('WEST')''

5.3.16 Utils

Utility functions useful across multiple modules.

Translation to/from SUIDs

edge_name_to_edge_suid(edge_names[, . . . ])edge_suid_to_edge_name(edge_suids[, . . . ])node_name_to_node_suid(node_names[, . . . ])node_suid_to_node_name(node_suids[, . . . ])

py4cytoscape.py4cytoscape_utils.edge_name_to_edge_suid

edge_name_to_edge_suid(edge_names, network=None, base_url='http://localhost:1234/v1')

py4cytoscape.py4cytoscape_utils.edge_suid_to_edge_name

edge_suid_to_edge_name(edge_suids, network=None, base_url='http://localhost:1234/v1')

py4cytoscape.py4cytoscape_utils.node_name_to_node_suid

node_name_to_node_suid(node_names, network=None, base_url='http://localhost:1234/v1')



py4cytoscape.py4cytoscape_utils.node_suid_to_node_name

node_suid_to_node_name(node_suids, network=None, base_url='http://localhost:1234/v1')

Miscellaneous

build_url([base_url, command]) Append a command (if it exists) to a base URLcyPalette([name])is_not_hex_color(color)table_column_exists(table_column, table[, . . . ])verify_supported_versions([cyrest, . . . ])

py4cytoscape.py4cytoscape_utils.build_url

build_url(base_url='http://localhost:1234/v1', command=None)Append a command (if it exists) to a base URL

py4cytoscape.py4cytoscape_utils.cyPalette

cyPalette(name='set1')

py4cytoscape.py4cytoscape_utils.is_not_hex_color

is_not_hex_color(color)

py4cytoscape.py4cytoscape_utils.table_column_exists

table_column_exists(table_column, table, network=None, base_url='http://localhost:1234/v1')

py4cytoscape.py4cytoscape_utils.verify_supported_versions

verify_supported_versions(cyrest=1, cytoscape=3.6, base_url='http://localhost:1234/v1')

5.4 Logging

py4cytoscape logging is based on the Python logging package, which is based on JUnit. py4cytoscape emits logentries in SysLog format. For example:

[INFO] py4...S: HTTP DELETE(http://localhost:1234/v1/networks)[INFO] py4...S: OK[200]

[INFO] is the priority level.

py4...S the name of the py4cytoscape package.

5.4. Logging 255


The count of | indicates the nesting level of the currently executing code, where || indicates log entries called fromcode at the | level.

The remainder of the message contains the logged information. In the example above, an HTTP DELETE call islogged along with the HTTP server’s reply.

Logger configuration is available in the py4cytoscape_logger_settings.py module. py4cytoscape emitstwo independent logging streams: Summary (to the console) and Detail (to a file in the logs directory).

By default, Summary logging is the short form (priority INFO), which shows HTTP calls and results. You can disableSummary logging by setting _SUMMARY_LOG_LEVEL to NOTSET, and you can enable full logging by setting it toDEBUG.

By default, Detail logging is the long form (priority DEBUG), and is controlled by the _DETAIL_LOG_LEVEL setting.

Here is an example of Detail logging involving nested calls:

2020-06-06 15:29:55,721 [DEBUG] py4...: Calling cytoscape_version_info(base_url=→˓'http://localhost:1234/v1')2020-06-06 15:29:55,721 [DEBUG] py4...: Calling cyrest_get('version', base_url='http:/→˓/localhost:1234/v1')2020-06-06 15:29:55,721 [DEBUG] py4...: HTTP GET(http://localhost:1234/v1/version)2020-06-06 15:29:55,737 [DEBUG] py4...: OK[200], content: {"apiVersion":"v1",→˓"cytoscapeVersion":"3.9.0-SNAPSHOT"}2020-06-06 15:29:55,738 [DEBUG] py4...: Returning 'cyrest_get': {'apiVersion': 'v1',→˓'cytoscapeVersion': '3.9.0-SNAPSHOT'}2020-06-06 15:29:55,738 [DEBUG] py4...: Returning 'cytoscape_version_info': {→˓'apiVersion': 'v1', 'cytoscapeVersion': '3.9.0-SNAPSHOT'}

5.4.1 Runtime Control

For convenience, Summary logging can be controlled using an environment variable or at execution time. By default,Summary logging is enabled, but can be disabled:

set PY4CYTOSCAPE_SUMMARY_LOGGER=False

At execution time, it can be disabled by calling set_summary_logger(). This is handy within a busy code blockor when running in a Notebook environment. For example:

old_state = set_summary_logger(False)# ... make several py4cytoscape calls ...

set_summary_logger(old_state)

5.5 Release Log

5.5.1 py4cytoscape 0.0.1

Release date: 01 Jan 2020

Initial release, matches API signatures for RCy3



Release notes

5.5.2 Announcement: py4cytoscape 0.0.1

We’re happy to announce the release of py4cytoscape 0.0.1!

. . . reword this to describe py4cytoscape modules . . .

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions ofcomplex networks.

For more information, please visit our website and our gallery of examples. Please send comments and questions tothe networkx-discuss mailing list.

5.5.3 Highlights

This release is the result of over two years of work with 1212 commits and 193 merges by 86 contributors. Highlightsinclude:

• We have made major changes to the methods in the Multi/Di/Graph classes. There is a migration guide forpeople moving from 1.X to 2.0.

• We updated the documentation system.

5.5.4 API Changes

• Base Graph Class Changes With the release of NetworkX 2.0 we are moving towards a view/iterator reportingAPI. We used to have two methods for the same property of the graph, one that returns a list and one thatreturns an iterator. With 2.0 we have replaced them with a view. A view is a read-only object that is quick tocreate, automatically updated, and provides basic access like iteration, membership and set operations whereappropriate. For example, G.nodes() used to return a list and G.nodes_iter() an iterator. Now G.nodes() returns a view and G.nodes_iter() is removed. G.degree() returns a view with (node,degree) iteration, so that dict(G.degree()) returns a dict keyed by node with degree as value. The oldbehavior

>>> G = nx.complete_graph(5)>>> G.nodes()[0, 1, 2, 3, 4]>>> G.nodes_iter()<dictionary-keyiterator at ...>

has changed to

>>> G = nx.complete_graph(5)>>> G.nodes()NodeView((0, 1, 2, 3, 4))>>> list(G.nodes())[0, 1, 2, 3, 4]

New feature include lookup of node and edge data from the views, property access without parentheses, and setoperations.

>>> G.add_node(3, color='blue')>>> G.nodes[3]{'color': 'blue'}

(continues on next page)

5.5. Release Log 257

http://networkx.github.io/

https://networkx.github.io/documentation/latest/auto_examples/index.html

http://groups.google.com/group/networkx-discuss

https://networkx.github.io/documentation/latest/release/migration_guide_from_1.x_to_2.0.html

https://networkx.github.io/documentation/latest/release/migration_guide_from_1.x_to_2.0.html


(continued from previous page)

>>> G.nodes & {3, 4, 5}{3, 4}

The following methods have changed:

– Graph/MultiGraph

* G.nodes()

* G.edges()

* G.neighbors()

* G.adjacency_list() and G.adjacency_iter() to G.adjacency()

* G.degree()

* G.subgraph()

* G.copy()

* G.__class__() should be replaced with G.fresh_copy()

– DiGraph/MultiDiGraph

* G.nodes()

* G.edges()

* G.in_edges()

* G.out_edges()

* G.degree()

* G.in_degree()

* G.out_degree()

* G.reverse()

The following deprecated methods will be removed in a future release (3.0?).

– G.node, G.edge (replaced by G.nodes, G.edges)

– G.add_path, G.add_cycle, G.add_star (Now nx.add_path(G,...)

– G.selfloop_edges, G.nodes_with_selfloops, G.number_of_selfloops (Nownx.selfloop_edges(G), etc)

Many subclasses have been changed accordingly such as:

– AntiGraph

– OrderedGraph and friends

– Examples such as ThinGraph that inherit from Graph

• [#2107] The Graph class methods add_edge and add_edges_from no longer allow the use of theattr_dict parameter. Instead use keyword arguments. Thus G.add_edge(1, 2, {'color':'red'}) becomes G.add_edge(1, 2, color='red'). Note that this only works if the attribute nameis a string. For non-string attributes you will need to add the edge and then update manually using e.g. G.edges[1, 2].update({0: "zero"})

• [#1577] In addition to minimum spanning trees, a new function for calculating maximum spanningtrees is now provided. The new API consists of four functions: minimum_spanning_edges,maximum_spanning_edges, minimum_spanning_tree, and maximum_spanning_tree. All of


https://github.com/networkx/networkx/pull/2107



these functions accept an algorithm parameter which specifies the algorithm to use when finding the min-imum or maximum spanning tree. Currently, Kruskal’s and Prim’s algorithms are implemented, defined as‘kruskal’ and ‘prim’, respectively. If nothing is specified, Kruskal’s algorithm is used. For example, to calculatethe maximum spanning tree of a graph using Kruskal’s algorithm, the function maximum_spanning_treehas to be called like:

>>> nx.maximum_spanning_tree(G, algorithm='kruskal')

The algorithm parameter is new and appears before the existing weight parameter. So existing code thatdid not explicitly name the optional weight parameter will need to be updated:

>>> nx.minimum_spanning_tree(G, 'mass') # old>>> nx.minimum_spanning_tree(G, weight='mass') # new

In the above, we are still relying on the the functions being imported into the top-level namespace. We do nothave immediate plans to deprecate this approach, but we recommend the following instead:

>>> from networkx.algorithms import tree# recommended>>> tree.minimum_spanning_tree(G, algorithm='kruskal', weight='mass')>>> tree.minimum_spanning_edges(G, algorithm='prim', weight='mass')

• [#1445] Most of the shortest_path algorithms now raise a NodeNotFound exception when a source ora target are not present in the graph.

• [#2326] Centrality algorithms were harmonized with respect to the default behavior of the weight parameter.The default value of the weight keyword argument has been changed from weight to None. This affects thefollowing centrality functions:

– approximate_current_flow_betweenness_centrality()

– current_flow_betweenness_centrality()

– current_flow_betweenness_centrality_subset()

– current_flow_closeness_centrality()

– edge_current_flow_betweenness_centrality()

– edge_current_flow_betweenness_centrality_subset()

– eigenvector_centrality()

– eigenvector_centrality_numpy()

– katz_centrality()

– katz_centrality_numpy()

• [#2420] New community detection algorithm provided. Fluid Communities is an asynchronous algorithm basedon the simple idea of fluids interacting in an environment, expanding and pushing each other. The algorithmis completely described in “Fluid Communities: A Competitive and Highly Scalable Community DetectionAlgorithm”.

• [#2510 and #2508] single_source_dijkstra, multi_source_dijkstra and functions that usethese now have new behavior when target is specified. Instead of returning dicts for distances and pathsa 2-tuple of (distance, path) is returned. When target is not specified the return value is still 2 dicts.

• [#2553] set_node_attributes() and set_edge_attributes() now accept dict-of-dict inputof shape {node/edge: {name: value}} in addition to previous valid inputs: {node/edge:value} and value. The order of the parameters changed also: The second parameter “values” is the valueargument and the third parameter “name” is the name of the attribute. “name” has default value None in which





https://arxiv.org/pdf/1703.09307.pdf

https://arxiv.org/pdf/1703.09307.pdf





case “values” must be the newly allowed form containing names. Previously “name” came second withoutdefault, and “values” came third.

• [#2604] Move selfloop methods out of base classes to networkx functions. G.number_of_selfloops(),G.selfloop_edges(), G.nodes_with_selfloops() are now nx.number_of_selfloops(G),nx.selfloop_edges(G), nx.nodes_with_selfloops(G).

G.node and G.edge are removed. Their functionality are replaced by G.nodes and G.edges.

• [#2558] Previously, the function from_pandas_dataframe assumed that the dataframe has edge-list like structures, but to_pandas_dataframe generates an adjacency matrix. We now providefour functions from_pandas_edgelist, to_pandas_edgelist, from_pandas_adjacency, andto_pandas_adjacency.

• [#2620] Removed draw_nx, please use draw or draw_networkx.

• [#1662] Rewrote topolgical_sort as a generator. It no longer accepts reverse or nbunch argumentsand is slightly faster. Added lexicographical_topological_sort, which accepts a key.

5.5.5 Deprecations

The following deprecated functions will be removed in 2.1.

• The function bellman_ford has been deprecated in favor of bellman_ford_predecessor_and_distance.

• The functions to_pandas_dataframe and from_pandas_dataframe have been deprecatedin favor of to_pandas_adjacency, from_pandas_adjacency, to_pandas_edgelist, andfrom_pandas_edgelist.

5.5.6 Contributors to this release

• Niels van Adrichem

• Kevin Arvai

• Ali Baharev

• Moritz Emanuel Beber

• Livio Bioglio

• Jake Bogerd

• Moreno Bonaventura

• Raphaël Bournhonesque

• Matthew Brett

• James Clough

• Marco Cognetta

• Jamie Cox

• Jon Crall

• Robert Davidson

• Nikhil Desai

• DonQuixoteDeLaMancha

• Dosenpfand







• Allen Downey

• Enrico

• Jens Erat

• Jeffrey Finkelstein

• Minas Gjoka

• Aravind Gollakota

• Thomas Grainger

• Aric Hagberg

• Harry

• Yawara ISHIDA

• Bilal AL JAMMAL

• Ryan James

• Omer Katz

• Janis Klaise

• Valentin Lorentz

• Alessandro Luongo

• Francois Malassenet

• Arya McCarthy

• Michael-E-Rose

• Peleg Michaeli

• Jarrod Millman

• Chris Morin

• Sanggyu Nam

• Nishant Nikhil

• Rhile Nova

• Ramil Nugmanov

• Juan Nunez-Iglesias

• Pim Otte

• Ferran Parés

• Richard Penney

• Phobia

• Tristan Poupard

• Sebastian Pucilowski

• Alexander Rodriguez

• Michael E. Rose

• Alex Ryan



• Zachary Sailer

• René Saitenmacher

• Felipe Schneider

• Dan Schult

• Scinawa

• Michael Seifert

• Mohammad Hossein Sekhavat

• Mridul Seth

• SkyTodInfi

• Stacey Smolash

• Jordi Torrents

• Martin Törnwall

• Jannis Vamvas

• Luca Verginer

• Prayag Verma

• Peter Wills

• Ianto Lin Xi

• Heqing Ya

• aryamccarthy

• chebee7i

• definitelyuncertain

• jfinkels

• juliensiebert

• leotrs

• leycec

• mcognetta

• numpde

• root

• salotz

• scott-vsi

• thegreathippo

• vpodpecan

• yash14123

• Neil Girdhar



5.5.7 Pull requests merged in this release

• Gml read fix. (#1962)

• Small changes leftover from #1847 (#1966)

• Fix k_core for directed graphs. Add tests (#1963)

• Communicability fix (#1958)

• Allows weight functions in shortest path functions (#1690)

• minor doc changes on weighted.py (#1969)

• Fix minimum_st_edge_cut documentation. (#1977)

• Fix all_node_cuts corner cases: cycle and complete graphs. (#1976)

• Change add_path/star/cycle from methods to functions (#1970)

• branch ‘edge-subgraph’ from @jfinkels (#1740)

• Corrected eppstein matching (#1955)

• Nose ignore docstrings (#1980)

• Edited Doc Makefile so clean doesn’t delete the examples folder (#1967)

• bug fix in convert_matrix.py (#1983)

• Avoid unnecessary eigenval sort in pagerank_numpy (#1986)

• Fix a typo in install.rst (#1991)

• Adds unorderable nodes test for dag_longest_path. (#1999)

• Improve drawing test scripts (typos, newlines, methods) (#1992)

• Improves test coverage for A* shortest path. (#1988)

• Improves test coverage for avg degree connectivity (#1987)

• Fix Graph() docstring to reflect input flexibility (#2006)

• Fix sphinx autosummary doc generation errors. (#2026)

• Improve gexf.py (#2010)

• Readme.rst should mention Decorator package is required. (#2009)

• fix_duplicate_kwarg: Fix a duplicate kwarg that was causing to_agraph. . . (#2005)

• Cleans documentation for graph6 and sparse6 I/O. (#2002)

• Remove http server example (#2001)

• Generalize and improve docstrings of node_link.py (#2000)

• fix issue #1948 and PEP8 formatting (#2031)

• Uses weight function for dijkstra_path_length. (#2033)

• Change default role for sphinx to ‘obj’ (#2027)

• fixed typo s/abritrary/arbitrary/ (#2035)

• Fix bug in dtype-valued matrices (#2038)

• Adds example for using Graph.nodes() with default (#2040)

• Clarifies some examples for relabel_nodes(). (#2041)



• Cleans code and documentation for graph power. (#2042)

• Cleans the classes.function module. (#2043)

• UnboundLocalError if called with an empty graph (#2047)

• Standardized Bellman-Ford function calls (#1910)

• Nobody is in IRC (#2059)

• Uses add_weighted_edges_from function in MST test. (#2061)

• Adds multi-source Dijkstra’s algorithm (#2073)

• Adds Voronoi cells algorithm (#2074)

• Fixes several issues with the Girvan-Newman partitioning function. Fixes #1703, #1725, #1799 (#1972)

• Moves is_path from utils to simple_paths. (#1921)

• add max_iter and tol parameter for numpy version (#2013)

• Remove draw_graphviz function. Fixes #1997 (#2077)

• Fixes #1998 edge_load function needs documentation. (#2075)

• Update fixcoverage.py (#2080)

• Support digraphs in approximate min vertex cover (#2039)

• Simplifies code in functions for greedy coloring. (#1680)

• Allows arbitrary metric in geometric generators. (#1679)

• Fix spring_layout for single node graph. (#2081)

• Updates set_{node,edge}_attributes and docs. (#1935)

• Fixes tests for maximal matching. (#1919)

• Adds LFM benchmark graph generator for communities (#1727)

• Adds global and local efficiency functions. (#1521)

• Apply alphas to individual nodes (#1289)

• Code and tests for temporal VF2 (#1653)

• extend convert_bool in gexf.py and graphml.py to all valid boolean (#1063)

• Remove encoded . . . to plain ascii (#2086)

• Use not_implemented_for() for in_degree_centrality() and out_degree_centrality() (#2084)

• Issue 2072 weighted modularity (#2088)

• Simplifies eigenvector centrality implementation. (#1708)

• Fjmalass nodes as tuples (#2089)

• Generator rename (#2090)

• Ensure links in doc `See also` sections (#2082)

• Document integer-only numeric mixing (#2085)

• doc sphinx error removal (#2091)

• Correct see also links (#2095)

• Adjust layout.py function signatures, docs, exposure (#2096)



• Adds missing __all__ attributes. (#2098)

• Fixes 2 bugs in dominance frontier code (#2092)

• Created two new files: joint_degree_seq.py and test_joint_degree_seq.. . . (#2011)

• Adds Boruvka’s minimum spanning tree algorithm. (#1873)

• Adds global/local reaching centrality functions. (#2099)

• Remove conflicts from #1894 (Update Exception Classes) (#2100)

• Add Exceptions for missing source in shortest_path (#2102)

• Docs for compose now warn about MultiGraph edgekeys (#2101)

• Improve Notes section on simplex and friends docs. (#2104)

• Add Dinitz’ algorithm for maximum flow problems. (#1978)

• Removed duplicated method/doc (add_edges_from) (#1)

• Bugfix for generic_multiedge_match (Issue #2114) (#2124)

• Fix for 2015. (#2)

• add_node, add_edge attr_dict change. (#2132)

• Handle graph name attribute in relabel_nodes (#2136)

• Fix fruchterman reingold bug and add more tests to layouts. (#2141)

• Adds exception: failed power iteration convergence (#2143)

• Tweak iteration logic of HITS (#2142)

• Fix PageRank personalize docstring (#2148)

• Set default source=None for dfs_tree (#2149)

• Fix docs for maximal_matching and tensor_product (#2158)

• Isolate edge key generation in multigraphs (#2150)

• Sort centralities together and outsource dispersion (#2083)

• Changed classic generators to use generators instead of lists (#2167)

• Adds beam search traversal algorithm with example (#2129)

• Turan graph (#2172)

• Removes irrelevant Notes section from docstring (#2178)

• Corrects logarithm base in example (#2179)

• Minor correction in documentation (#2180)

• Add Boykov Kolmogorov algorithm for maximum flow problems. (#2122)

• Remove temporary files after tests are run. (#2202)

• Add support for subgraphs with no edges in convert_matrix.to_scipy_sparse_matrix. (#2199)

• Add support for reading adjacency matrix in readwrite.pajek.parse_pajek. (#2200)

• Moves Graph Atlas to data file. (#2064)

• Refactor Dinitz’ algorithm implementation. (#2196)

• Use arrays instead of matrices in scipy.linalg.expm() (#2208)



• Making in_edges equivalent to out_edges (#2206)

• Fix tests failing because of ordering issues. (#2207)

• Fix code escaping. (#2214)

• Add adjlist_outer_dict_factory. (#2222)

• Typo in scale free network generator documentation (#2225)

• Add link to nx.drawing.layout instead of mentionning nx.layout. (#2224)

• Example not working in tutorial (#2230)

• don’t assume nodes are sortable when running dag_longest_path (#2228)

• Correct typo (#2236)

• Use ego graph when computing local efficiency (#2246)

• Make harmonic centrality more memory-efficient (#2247)

• have dag_longest_path_length return path length, not edge count (#2237)

• Added transitive_reduction in dag (#2215)

• alpha kwarg not used in pylab label drawing, added it here. (#2269)

• Make PyDot Support Great Again (#2272)

• Unnecessary array copying in katz_centrality_numpy ? (#2287)

• Switch to faster smallest-last algorithm implementation. (#2268)

• Adds example for getting all simple edge paths. Fixes #718 (#2260)

• Remove obsolete testing tools. (#2303)

• Correct error in minimum_spanning_arborescence (#2285)

• Yield string, not dict, in dfs_labeled_edges. (#2277)

• Removes unnecessary convert_to_(un)directed func (#2259)

• Complete multipartite graph docs (#2221)

• fix LPA bug, see issues/2219 (#2227)

• Generalized degree (#2220)

• Turan docs (#2218)

• Fix broken link to the description of the P2G format. (#2211)

• Test ordering (#2209)

• add example of node weights (#2250)

• added paramether nbunch (#2253)

• Adds unit tests for using dtype with to_numpy_matrix (#2257)

• Adds chain decomposition algorithm. (#2284)

• add the Hoffman-Singleton graph (#2275)

• Allow grid_graph generator to accept tuple dim argument (#2320)

• psuedo -> pseudo (fixing typo) (#2322)

• Corrects navigable small world graph param docs (#2321)



• Fix bug in find_cycle. (#2324)

• flip source target (#2309)

• Simpler version of digitsrep(..) function (#2330)

• change articulation_points so that it only returns every vertex once (#2333)

• Use faster random geometric graph implementation. (#2337)

• Allow community asyn_lpa test to have two answers (#2339)

• Fix broken links and remove pdf files from Makefile (#2344)

• Documents orderable node requirement for isom. (#2302)

• Adds modularity measure for communities. (#1729)

• Simplifies degree sequence graph generators. (#1866)

• Adds tree encoding and decoding functions. (#1874)

• Corrects number_of_edges docs for directed graphs (#2360)

• Adds multigraph keys to Eulerian circuits (#2359)

• Update predecessors/successors in edge subgraph (#2373)

• Fix for #2364 (#2372)

• Raise an Exception for disconnected Graphs in bipartite.sets (#2375)

• fixes typo in NetworkXNotImplemented (#2385)

• Check alternating paths using iterative DFS in to_vertex_cover. (#2386)

• Fix typos in generating NXError in networkx.linalg.graphmatrix.incidence_matrix (#2395)

• [Fixes #2342] remove calls to plt.hold(), deprecated in mpl2.0 (#2397)

• Fix broken links (#2414)

• Fix all tests for 3.6 (#2413)

• Improve bipartite documentation. (#2402)

• correct logic in GEXFWriter (#2399)

• list optional dependencies in setup.py (#2398)

• Gitwash update (#2371)

• Added cytoscape JSON handling (#2351)

• Fix for issues #2328 and #2332 (#2366)

• Workaround for gdal python3.6 at travis and more doctests fixes (#2416)

• Fixed bug on custom attrs usage: unavailable iteritems method for dict. (#2461)

• Fix sphinx errors and class outlines (#2480)

• Note the precondition that graphs are directed and acyclic (#2500)

• Add CONTRIBUTE file (#2501)

• Remove external module (#2521)

• Ensure make html doesn’t fail build on exit (#2530)

• Cherry pick missing commits (#2535)



• Document release process (#2539)

• Update copyright (#2551)

• Remove deprecated code (#2536)

• Improve docs (#2555)

• WIP: Add note on how to estimate appropriate values for alpha (#2583)

• Travis refactor (#2596)

• Create separate functions for df as edge-lists and adjacency matrices (#2558)

• Use texext for math_dollar (#2609)

• Add drawing tests (#2617)

• Add threshold tests (#2622)

• Update docs (#2623)

• Prep beta release (#2624)

• Refactor travis tests and deploy docs with travis (#2647)

• matplotlib 2.1 deprecated is_string_like (#2659)

• topolgical_sort, lexicographical_topological_sort (#1662)

5.6 License

Released under the MIT License:

Copyright (c) 2018-2020 The Cytoscape ConsortiumBarry Demchak <[email protected]>

Permission is hereby granted, free of charge, to any person obtaining a copy of thissoftware and associated documentation files (the "Software"), to deal in the Softwarewithout restriction, including without limitation the rights to use, copy, modify,merge, publish, distribute, sublicense, and/or sell copies of the Software, and topermit persons to whom the Software is furnished to do so, subject to the followingconditions:

The above copyright notice and this permission notice shall be included in all copiesor substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR APARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHTHOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTIONOF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THESOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.



5.7 Credits

py4cytoscape was originally written by Barry Demchak with the help of many others, particularly the developersof RCy3, on which py4cytoscape is based. Thanks to everyone who has improved py4cytoscape by contribut-ing code, bug reports (and fixes), documentation, and input on design, features, and the future of py4cytoscape.

5.7.1 Contributions

This section aims to provide a list of people and projects that have contributed to py4cytoscape. It is intended tobe an inclusive list, and anyone who has contributed and wishes to make that contribution known is welcome to addan entry into this file. Generally, no name should be added to this list without the approval of the person associatedwith that name.

Creating a comprehensive list of contributors can be difficult, and the list within this file is almost certainly incomplete.Contributors include testers, bug reporters, contributors who wish to remain anonymous, funding sources, academicadvisors, end users, and even build/integration systems.

Do you want to make your contribution known? If you have commit access, edit this file and add your name. If youdo not have commit access, feel free to open an issue, submit a pull request, or get in contact with one of the officialteam members.

Original Authors

Keiichiro OnoJorge BouçasKozo NishidaBarry Demchak

Contributors

Optionally, add your desired name and include a few relevant links. The order is partially historical, and now, mostlyarbitrary.

• Keiichiro Ono, GitHub: keiono

• Jorge Bouças, GitHub: jorgeboucas

• Kozo Nishida, GitHub: kozo2

• Barry Demchak, GitHub: bdemchak

• Alex Pico, GitHub: AlexanderPico

• Mark Grimes, GitHub: mark-grimes

• Julia Gustavsen, GitHub: jooolia

• Shraddha Pai, GitHub: shraddhapai

• Ruth Isserlin, GitHub: risserlin

• Paul Shannon, GitHub: paul-shannon

• Tanja Muetze, GitHub: tmuetze

• Georgi Kolishkovski

• David Otasek

5.7. Credits 269

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880260/

https://github.com/bdemchak/py4cytoscape/issues/new

https://github.com/bdemchak/py4cytoscape/compare/

https://github.com/bdemchak?tab=members

https://github.com/keiono

https://github.com/jorgeboucas

https://github.com/kozo2

https://github.com/bdemchak

https://github.com/AlexanderPico

https://github.com/mark-grimes

https://github.com/jooolia

https://github.com/shraddhapai

https://github.com/risserlin

https://github.com/paul-shannon/

https://github.com/tmuetze


The NetworkX documentation is excellent, and we borrowed both wording and structure liberally.

5.7.2 Support

py4cytoscape and those who have contributed to py4cytoscape have received support throughout the yearsfrom a variety of sources. We list them below. If you have provided support to py4cytoscape and a supportacknowledgment does not appear below, please help us remedy the situation, and similarly, please let us know if you’dlike something modified or corrected.

Funding

py4cytoscape acknowledges support from the following:

• US National Institute of General Medical Sciences (NIGMS), award number R01 GM070743, PI: Trey Ideker

• National Resource for Network Biology (NRNB), award number P41 GM103504, PI: Trey Ideker

• Torrey Pines Software, Inc, President: Barry Demchak

5.8 Citing

There is no paper (yet) that describes py4cytoscape.


https://networkx.github.io/

http://www.nigms.nih.gov/

http://nrnb.org/

http://tpsoft.com/

CHAPTER

SIX

INDICES AND TABLES

• genindex

• modindex

• search

271


272 Chapter 6. Indices and tables

PYTHON MODULE INDEX

ppy4cytoscape.apps, 14py4cytoscape.collections, 21py4cytoscape.commands, 23py4cytoscape.cy_ndex, 33py4cytoscape.cytoscape_system, 37py4cytoscape.exceptions, 40py4cytoscape.filters, 40py4cytoscape.groups, 46py4cytoscape.layouts, 54py4cytoscape.network_selection, 81py4cytoscape.network_views, 96py4cytoscape.networks, 61py4cytoscape.py4cytoscape_utils, 254py4cytoscape.session, 101py4cytoscape.style_bypasses, 111py4cytoscape.style_defaults, 151py4cytoscape.style_dependencies, 187py4cytoscape.style_mappings, 191py4cytoscape.style_values, 225py4cytoscape.styles, 103py4cytoscape.tables, 237py4cytoscape.tools, 245py4cytoscape.user_interface, 251

273


274 Python Module Index

INDEX

Aadd_cy_edges() (in module py4cytoscape.networks),

64add_cy_nodes() (in module py4cytoscape.networks),

61add_to_group() (in module py4cytoscape.groups),

46apply_filter() (in module py4cytoscape.filters), 40

Bbuild_url() (in module

py4cytoscape.py4cytoscape_utils), 255bundle_edges() (in module py4cytoscape.layouts),

54

Cclear_edge_bends() (in module

py4cytoscape.layouts), 55clear_edge_property_bypass() (in module

py4cytoscape.style_bypasses), 131clear_network_center_bypass() (in module

py4cytoscape.style_bypasses), 146clear_network_property_bypass() (in mod-

ule py4cytoscape.style_bypasses), 147clear_network_zoom_bypass() (in module

py4cytoscape.style_bypasses), 147clear_node_opacity_bypass() (in module

py4cytoscape.style_bypasses), 114clear_node_property_bypass() (in module

py4cytoscape.style_bypasses), 114clear_selection() (in module

py4cytoscape.network_selection), 81clone_network() (in module

py4cytoscape.networks), 68close_session() (in module py4cytoscape.session),

101collapse_group() (in module

py4cytoscape.groups), 51command_echo() (in module

py4cytoscape.commands), 29command_open_dialog() (in module

py4cytoscape.commands), 30

command_pause() (in modulepy4cytoscape.commands), 30

command_quit() (in modulepy4cytoscape.commands), 31

command_run_file() (in modulepy4cytoscape.commands), 31

command_sleep() (in modulepy4cytoscape.commands), 32

commands_api() (in modulepy4cytoscape.commands), 32

commands_get() (in modulepy4cytoscape.commands), 27

commands_help() (in modulepy4cytoscape.commands), 27

commands_post() (in modulepy4cytoscape.commands), 28

commands_run() (in modulepy4cytoscape.commands), 29

copy_visual_style() (in modulepy4cytoscape.styles), 104

create_column_filter() (in modulepy4cytoscape.filters), 43

create_composite_filter() (in modulepy4cytoscape.filters), 44

create_degree_filter() (in modulepy4cytoscape.filters), 45

create_group() (in module py4cytoscape.groups),47

create_group_by_column() (in modulepy4cytoscape.groups), 48

create_igraph_from_network() (in modulepy4cytoscape.networks), 75

create_network_from_data_frames() (inmodule py4cytoscape.networks), 76

create_network_from_igraph() (in modulepy4cytoscape.networks), 77

create_network_from_networkx() (in modulepy4cytoscape.networks), 78

create_networkx_from_network() (in modulepy4cytoscape.networks), 79

create_subnetwork() (in modulepy4cytoscape.networks), 68

275


create_visual_style() (in modulepy4cytoscape.styles), 104

cybrowser_close() (in module py4cytoscape.tools),245

cybrowser_dialog() (in modulepy4cytoscape.tools), 246

cybrowser_hide() (in module py4cytoscape.tools),246

cybrowser_list() (in module py4cytoscape.tools),247

cybrowser_send() (in module py4cytoscape.tools),248

cybrowser_show() (in module py4cytoscape.tools),248

cybrowser_version() (in modulepy4cytoscape.tools), 249

CyError, 40cyPalette() (in module

py4cytoscape.py4cytoscape_utils), 255cyrest_api() (in module py4cytoscape.commands),

33cyrest_delete() (in module

py4cytoscape.commands), 24cyrest_get() (in module py4cytoscape.commands),

25cyrest_post() (in module py4cytoscape.commands),

25cyrest_put() (in module py4cytoscape.commands),

26cytoscape_api_versions() (in module

py4cytoscape.cytoscape_system), 38cytoscape_free_memory() (in module

py4cytoscape.cytoscape_system), 37cytoscape_memory_status() (in module

py4cytoscape.cytoscape_system), 37cytoscape_number_of_cores() (in module

py4cytoscape.cytoscape_system), 38cytoscape_ping() (in module

py4cytoscape.cytoscape_system), 39cytoscape_version_info() (in module

py4cytoscape.cytoscape_system), 39

Ddelete_all_networks() (in module

py4cytoscape.networks), 69delete_duplicate_edges() (in module

py4cytoscape.network_selection), 88delete_group() (in module py4cytoscape.groups),

49delete_network() (in module

py4cytoscape.networks), 70delete_selected_edges() (in module

py4cytoscape.network_selection), 89

delete_selected_nodes() (in modulepy4cytoscape.network_selection), 82

delete_self_loops() (in modulepy4cytoscape.network_selection), 90

delete_style_mapping() (in modulepy4cytoscape.style_mappings), 192

delete_table_column() (in modulepy4cytoscape.tables), 237

delete_visual_style() (in modulepy4cytoscape.styles), 105

diffusion_advanced() (in modulepy4cytoscape.tools), 250

diffusion_basic() (in module py4cytoscape.tools),251

disable_app() (in module py4cytoscape.apps), 14dock_panel() (in module

py4cytoscape.user_interface), 251

Eedge_name_to_edge_suid() (in module

py4cytoscape.py4cytoscape_utils), 254edge_suid_to_edge_name() (in module

py4cytoscape.py4cytoscape_utils), 254enable_app() (in module py4cytoscape.apps), 15expand_group() (in module py4cytoscape.groups),

52export_filters() (in module py4cytoscape.filters),

41export_image() (in module

py4cytoscape.network_views), 96export_network() (in module

py4cytoscape.networks), 80export_network_to_ndex() (in module

py4cytoscape.cy_ndex), 34export_visual_styles() (in module

py4cytoscape.styles), 106

Ffit_content() (in module

py4cytoscape.network_views), 97float_panel() (in module

py4cytoscape.user_interface), 252

Gget_all_edges() (in module

py4cytoscape.networks), 65get_all_nodes() (in module

py4cytoscape.networks), 62get_app_information() (in module

py4cytoscape.apps), 19get_app_status() (in module py4cytoscape.apps),

15get_app_updates() (in module py4cytoscape.apps),

16

276 Index


get_arrow_shapes() (in modulepy4cytoscape.styles), 109

get_available_apps() (in modulepy4cytoscape.apps), 20

get_background_color_default() (in modulepy4cytoscape.style_defaults), 186

get_collection_list() (in modulepy4cytoscape.collections), 21

get_collection_name() (in modulepy4cytoscape.collections), 22

get_collection_networks() (in modulepy4cytoscape.collections), 22

get_collection_suid() (in modulepy4cytoscape.collections), 23

get_disabled_apps() (in modulepy4cytoscape.apps), 16

get_edge_color() (in modulepy4cytoscape.style_values), 231

get_edge_count() (in modulepy4cytoscape.networks), 66

get_edge_info() (in modulepy4cytoscape.networks), 66

get_edge_line_style() (in modulepy4cytoscape.style_values), 231

get_edge_line_width() (in modulepy4cytoscape.style_values), 232

get_edge_property() (in modulepy4cytoscape.style_values), 233

get_edge_selection_color_default() (inmodule py4cytoscape.style_defaults), 176

get_edge_target_arrow_shape() (in modulepy4cytoscape.style_values), 234

get_filter_list() (in modulepy4cytoscape.filters), 42

get_first_neighbors() (in modulepy4cytoscape.networks), 63

get_group_info() (in modulepy4cytoscape.groups), 52

get_installed_apps() (in modulepy4cytoscape.apps), 17

get_layout_name_mapping() (in modulepy4cytoscape.layouts), 57

get_layout_names() (in modulepy4cytoscape.layouts), 58

get_layout_property_names() (in modulepy4cytoscape.layouts), 58

get_layout_property_type() (in modulepy4cytoscape.layouts), 59

get_layout_property_value() (in modulepy4cytoscape.layouts), 59

get_line_styles() (in modulepy4cytoscape.styles), 109

get_network_center() (in modulepy4cytoscape.style_values), 235

get_network_count() (in modulepy4cytoscape.networks), 70

get_network_list() (in modulepy4cytoscape.networks), 71

get_network_name() (in modulepy4cytoscape.networks), 71

get_network_ndex_id() (in modulepy4cytoscape.cy_ndex), 36

get_network_property() (in modulepy4cytoscape.style_values), 235

get_network_suid() (in modulepy4cytoscape.networks), 72

get_network_view_suid() (in modulepy4cytoscape.network_views), 98

get_network_views() (in modulepy4cytoscape.network_views), 99

get_network_zoom() (in modulepy4cytoscape.style_values), 236

get_node_color() (in modulepy4cytoscape.style_values), 226

get_node_count() (in modulepy4cytoscape.networks), 64

get_node_height() (in modulepy4cytoscape.style_values), 226

get_node_position() (in modulepy4cytoscape.style_values), 227

get_node_property() (in modulepy4cytoscape.style_values), 228

get_node_selection_color_default() (inmodule py4cytoscape.style_defaults), 164

get_node_shapes() (in modulepy4cytoscape.styles), 110

get_node_size() (in modulepy4cytoscape.style_values), 229

get_node_width() (in modulepy4cytoscape.style_values), 230

get_selected_edge_count() (in modulepy4cytoscape.network_selection), 91

get_selected_edges() (in modulepy4cytoscape.network_selection), 91

get_selected_node_count() (in modulepy4cytoscape.network_selection), 83

get_selected_nodes() (in modulepy4cytoscape.network_selection), 83

get_style_all_mappings() (in modulepy4cytoscape.style_mappings), 192

get_style_dependencies() (in modulepy4cytoscape.style_dependencies), 188

get_style_mapping() (in modulepy4cytoscape.style_mappings), 193

get_table_column_names() (in modulepy4cytoscape.tables), 238

get_table_column_types() (in modulepy4cytoscape.tables), 239

Index 277


get_table_columns() (in modulepy4cytoscape.tables), 239

get_table_value() (in modulepy4cytoscape.tables), 243

get_uninstalled_apps() (in modulepy4cytoscape.apps), 17

get_visual_property_default() (in modulepy4cytoscape.style_defaults), 152

get_visual_property_names() (in modulepy4cytoscape.styles), 110

get_visual_style_names() (in modulepy4cytoscape.styles), 107

Hhide_all_panels() (in module

py4cytoscape.user_interface), 253hide_edges() (in module

py4cytoscape.style_bypasses), 132hide_nodes() (in module

py4cytoscape.style_bypasses), 115hide_panel() (in module

py4cytoscape.user_interface), 253hide_selected_edges() (in module

py4cytoscape.style_bypasses), 133hide_selected_nodes() (in module

py4cytoscape.style_bypasses), 116

Iimport_filters() (in module py4cytoscape.filters),

42import_network_from_file() (in module

py4cytoscape.networks), 80import_network_from_ndex() (in module

py4cytoscape.cy_ndex), 34import_visual_styles() (in module

py4cytoscape.styles), 107install_app() (in module py4cytoscape.apps), 18invert_edge_selection() (in module

py4cytoscape.network_selection), 92invert_node_selection() (in module

py4cytoscape.network_selection), 84is_not_hex_color() (in module

py4cytoscape.py4cytoscape_utils), 255

Llayout_copycat() (in module

py4cytoscape.layouts), 55layout_network() (in module

py4cytoscape.layouts), 56list_groups() (in module py4cytoscape.groups), 53load_table_data() (in module

py4cytoscape.tables), 244lock_node_dimensions() (in module

py4cytoscape.style_dependencies), 190

Mmap_table_column() (in module

py4cytoscape.tables), 242map_visual_property() (in module

py4cytoscape.style_mappings), 194match_arrow_color_to_edge() (in module

py4cytoscape.style_dependencies), 191module

py4cytoscape.apps, 14py4cytoscape.collections, 21py4cytoscape.commands, 23py4cytoscape.cy_ndex, 33py4cytoscape.cytoscape_system, 37py4cytoscape.exceptions, 40py4cytoscape.filters, 40py4cytoscape.groups, 46py4cytoscape.layouts, 54py4cytoscape.network_selection, 81py4cytoscape.network_views, 96py4cytoscape.networks, 61py4cytoscape.py4cytoscape_utils, 254py4cytoscape.session, 101py4cytoscape.style_bypasses, 111py4cytoscape.style_defaults, 151py4cytoscape.style_dependencies, 187py4cytoscape.style_mappings, 191py4cytoscape.style_values, 225py4cytoscape.styles, 103py4cytoscape.tables, 237py4cytoscape.tools, 245py4cytoscape.user_interface, 251

Nnode_name_to_node_suid() (in module

py4cytoscape.py4cytoscape_utils), 254node_suid_to_node_name() (in module


Oopen_app_store() (in module py4cytoscape.apps),

20open_session() (in module py4cytoscape.session),

102

Ppy4cytoscape.apps

module, 14py4cytoscape.collections

module, 21py4cytoscape.commands

module, 23py4cytoscape.cy_ndex

module, 33py4cytoscape.cytoscape_system

278 Index


module, 37py4cytoscape.exceptions

module, 40py4cytoscape.filters

module, 40py4cytoscape.groups

module, 46py4cytoscape.layouts

module, 54py4cytoscape.network_selection

module, 81py4cytoscape.network_views

module, 96py4cytoscape.networks

module, 61py4cytoscape.py4cytoscape_utils

module, 254py4cytoscape.session

module, 101py4cytoscape.style_bypasses

module, 111py4cytoscape.style_defaults

module, 151py4cytoscape.style_dependencies

module, 187py4cytoscape.style_mappings

module, 191py4cytoscape.style_values

module, 225py4cytoscape.styles

module, 103py4cytoscape.tables

module, 237py4cytoscape.tools

module, 245py4cytoscape.user_interface

module, 251

Rremove_from_group() (in module

py4cytoscape.groups), 50remove_node_custom_graphics() (in module

py4cytoscape.style_defaults), 154rename_network() (in module

py4cytoscape.networks), 73rename_table_column() (in module

py4cytoscape.tables), 241

Ssave_session() (in module py4cytoscape.session),

102select_all_edges() (in module

py4cytoscape.network_selection), 93

select_all_nodes() (in modulepy4cytoscape.network_selection), 85

select_edges() (in modulepy4cytoscape.network_selection), 93

select_edges_adjacent_to_selected_nodes()(in module py4cytoscape.network_selection),94

select_edges_connecting_selected_nodes()(in module py4cytoscape.network_selection),95

select_first_neighbors() (in modulepy4cytoscape.network_selection), 86

select_nodes() (in modulepy4cytoscape.network_selection), 86

select_nodes_connected_by_selected_edges()(in module py4cytoscape.network_selection),87

set_background_color_default() (in modulepy4cytoscape.style_defaults), 187

set_current_network() (in modulepy4cytoscape.networks), 74

set_current_view() (in modulepy4cytoscape.network_views), 99

set_edge_color_bypass() (in modulepy4cytoscape.style_bypasses), 134

set_edge_color_default() (in modulepy4cytoscape.style_defaults), 176

set_edge_color_mapping() (in modulepy4cytoscape.style_mappings), 212

set_edge_font_face_bypass() (in modulepy4cytoscape.style_bypasses), 134

set_edge_font_face_default() (in modulepy4cytoscape.style_defaults), 177

set_edge_font_face_mapping() (in modulepy4cytoscape.style_mappings), 212

set_edge_font_size_bypass() (in modulepy4cytoscape.style_bypasses), 135

set_edge_font_size_default() (in modulepy4cytoscape.style_defaults), 178

set_edge_font_size_mapping() (in modulepy4cytoscape.style_mappings), 213

set_edge_label_bypass() (in modulepy4cytoscape.style_bypasses), 136

set_edge_label_color_bypass() (in modulepy4cytoscape.style_bypasses), 137

set_edge_label_color_default() (in modulepy4cytoscape.style_defaults), 178

set_edge_label_color_mapping() (in modulepy4cytoscape.style_mappings), 214

set_edge_label_default() (in modulepy4cytoscape.style_defaults), 179

set_edge_label_mapping() (in modulepy4cytoscape.style_mappings), 215

set_edge_label_opacity_bypass() (in mod-

Index 279


ule py4cytoscape.style_bypasses), 138set_edge_label_opacity_default() (in mod-

ule py4cytoscape.style_defaults), 179set_edge_label_opacity_mapping() (in mod-

ule py4cytoscape.style_mappings), 216set_edge_line_style_bypass() (in module

py4cytoscape.style_bypasses), 138set_edge_line_style_default() (in module

py4cytoscape.style_defaults), 180set_edge_line_style_mapping() (in module

py4cytoscape.style_mappings), 217set_edge_line_width_bypass() (in module

py4cytoscape.style_bypasses), 139set_edge_line_width_default() (in module

py4cytoscape.style_defaults), 181set_edge_line_width_mapping() (in module

py4cytoscape.style_mappings), 217set_edge_opacity_bypass() (in module

py4cytoscape.style_bypasses), 140set_edge_opacity_default() (in module

py4cytoscape.style_defaults), 181set_edge_opacity_mapping() (in module

py4cytoscape.style_mappings), 218set_edge_property_bypass() (in module

py4cytoscape.style_bypasses), 112set_edge_selection_color_default() (in

module py4cytoscape.style_defaults), 182set_edge_source_arrow_color_bypass() (in

module py4cytoscape.style_bypasses), 141set_edge_source_arrow_color_default()

(in module py4cytoscape.style_defaults), 183set_edge_source_arrow_color_mapping()

(in module py4cytoscape.style_mappings), 219set_edge_source_arrow_mapping() (in mod-

ule py4cytoscape.style_mappings), 220set_edge_source_arrow_shape_bypass() (in

module py4cytoscape.style_bypasses), 142set_edge_source_arrow_shape_default()

(in module py4cytoscape.style_defaults), 183set_edge_source_arrow_shape_mapping()

(in module py4cytoscape.style_mappings), 221set_edge_target_arrow_color_bypass() (in

module py4cytoscape.style_bypasses), 142set_edge_target_arrow_color_default()

(in module py4cytoscape.style_defaults), 184set_edge_target_arrow_color_mapping()

(in module py4cytoscape.style_mappings), 222set_edge_target_arrow_maping() (in module

py4cytoscape.style_mappings), 223set_edge_target_arrow_shape_bypass() (in

module py4cytoscape.style_bypasses), 143set_edge_target_arrow_shape_default()

(in module py4cytoscape.style_defaults), 185set_edge_target_arrow_shape_mapping()

(in module py4cytoscape.style_mappings), 224set_edge_tooltip_bypass() (in module

py4cytoscape.style_bypasses), 144set_edge_tooltip_default() (in module

py4cytoscape.style_defaults), 185set_edge_tooltip_mapping() (in module

py4cytoscape.style_mappings), 225set_layout_properties() (in module

py4cytoscape.layouts), 60set_network_center_bypass() (in module

py4cytoscape.style_bypasses), 148set_network_property_bypass() (in module

py4cytoscape.style_bypasses), 149set_network_zoom_bypass() (in module

py4cytoscape.style_bypasses), 150set_node_border_color_bypass() (in module

py4cytoscape.style_bypasses), 117set_node_border_color_default() (in mod-

ule py4cytoscape.style_defaults), 165set_node_border_color_mapping() (in mod-

ule py4cytoscape.style_mappings), 197set_node_border_opacity_bypass() (in mod-

ule py4cytoscape.style_bypasses), 118set_node_border_opacity_default() (in

module py4cytoscape.style_defaults), 165set_node_border_opacity_mapping() (in

module py4cytoscape.style_mappings), 198set_node_border_width_bypass() (in module

py4cytoscape.style_bypasses), 118set_node_border_width_default() (in mod-

ule py4cytoscape.style_defaults), 166set_node_border_width_mapping() (in mod-

ule py4cytoscape.style_mappings), 199set_node_color_bypass() (in module

py4cytoscape.style_bypasses), 119set_node_color_default() (in module

py4cytoscape.style_defaults), 167set_node_color_mapping() (in module

py4cytoscape.style_mappings), 200set_node_combo_opacity_mapping() (in mod-

ule py4cytoscape.style_mappings), 201set_node_custom_bar_chart() (in module

py4cytoscape.style_defaults), 155set_node_custom_box_chart() (in module

py4cytoscape.style_defaults), 156set_node_custom_heat_map_chart() (in mod-

ule py4cytoscape.style_defaults), 157set_node_custom_line_chart() (in module

py4cytoscape.style_defaults), 158set_node_custom_linear_gradient() (in

module py4cytoscape.style_defaults), 159set_node_custom_pie_chart() (in module

py4cytoscape.style_defaults), 160set_node_custom_position() (in module

280 Index


py4cytoscape.style_defaults), 161set_node_custom_radial_gradient() (in

module py4cytoscape.style_defaults), 162set_node_custom_ring_chart() (in module

py4cytoscape.style_defaults), 163set_node_fill_opacity_bypass() (in module

py4cytoscape.style_bypasses), 120set_node_fill_opacity_default() (in mod-

ule py4cytoscape.style_defaults), 167set_node_fill_opacity_mapping() (in mod-

ule py4cytoscape.style_mappings), 202set_node_font_face_bypass() (in module

py4cytoscape.style_bypasses), 121set_node_font_face_default() (in module

py4cytoscape.style_defaults), 168set_node_font_face_mapping() (in module

py4cytoscape.style_mappings), 203set_node_font_size_bypass() (in module

py4cytoscape.style_bypasses), 122set_node_font_size_default() (in module

py4cytoscape.style_defaults), 169set_node_font_size_mapping() (in module

py4cytoscape.style_mappings), 204set_node_height_bypass() (in module

py4cytoscape.style_bypasses), 122set_node_height_default() (in module

py4cytoscape.style_defaults), 169set_node_height_mapping() (in module

py4cytoscape.style_mappings), 205set_node_label_bypass() (in module

py4cytoscape.style_bypasses), 123set_node_label_color_bypass() (in module

py4cytoscape.style_bypasses), 124set_node_label_color_default() (in module

py4cytoscape.style_defaults), 170set_node_label_color_mapping() (in module

py4cytoscape.style_mappings), 206set_node_label_default() (in module

py4cytoscape.style_defaults), 171set_node_label_mapping() (in module

py4cytoscape.style_mappings), 207set_node_label_opacity_bypass() (in mod-

ule py4cytoscape.style_bypasses), 125set_node_label_opacity_default() (in mod-

ule py4cytoscape.style_defaults), 171set_node_label_opacity_mapping() (in mod-

ule py4cytoscape.style_mappings), 207set_node_opacity_bypass() (in module

py4cytoscape.style_bypasses), 126set_node_property_bypass() (in module

py4cytoscape.style_bypasses), 111set_node_selection_color_default() (in

module py4cytoscape.style_defaults), 172set_node_shape_bypass() (in module

py4cytoscape.style_bypasses), 126set_node_shape_default() (in module

py4cytoscape.style_defaults), 173set_node_shape_mapping() (in module

py4cytoscape.style_mappings), 208set_node_size_bypass() (in module

py4cytoscape.style_bypasses), 127set_node_size_default() (in module

py4cytoscape.style_defaults), 173set_node_size_mapping() (in module

py4cytoscape.style_mappings), 209set_node_tooltip_bypass() (in module

py4cytoscape.style_bypasses), 128set_node_tooltip_default() (in module

py4cytoscape.style_defaults), 174set_node_tooltip_mapping() (in module

py4cytoscape.style_mappings), 210set_node_width_bypass() (in module

py4cytoscape.style_bypasses), 129set_node_width_default() (in module

py4cytoscape.style_defaults), 175set_node_width_mapping() (in module

py4cytoscape.style_mappings), 211set_style_dependencies() (in module

py4cytoscape.style_dependencies), 188set_visual_property_default() (in module

py4cytoscape.style_defaults), 152set_visual_style() (in module

py4cytoscape.styles), 108sync_node_custom_graphics_size() (in mod-

ule py4cytoscape.style_dependencies), 189

Ttable_column_exists() (in module

py4cytoscape.py4cytoscape_utils), 255toggle_graphics_details() (in module

py4cytoscape.network_views), 100

Uunhide_all() (in module

py4cytoscape.style_bypasses), 151unhide_edges() (in module

py4cytoscape.style_bypasses), 145unhide_nodes() (in module

py4cytoscape.style_bypasses), 130uninstall_app() (in module py4cytoscape.apps), 18update_app() (in module py4cytoscape.apps), 19update_network_in_ndex() (in module

py4cytoscape.cy_ndex), 35update_style_defaults() (in module

py4cytoscape.style_defaults), 153update_style_mapping() (in module

py4cytoscape.style_mappings), 195

Index 281


Vverify_supported_versions() (in module


282 Index

Date post:	20-Jan-2023
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