48
Page 1 of 48 ioGAS Quick Start Tutorial
| Date post: | 04-Aug-2018 |
| Category: |
Documents |
| Upload: | nguyenduong |
| View: | 218 times |
| Download: | 0 times |
Page 1 of 48
ioGAS
Quick Start Tutorial
Page 2 of 48
Contents
1. Import Data................................................................................................................................................................ 5
Open Excel File ........................................................................................................................................................... 5
2. Define Column Types ................................................................................................................................................. 7
Special Columns ......................................................................................................................................................... 7
Column Name and Type ............................................................................................................................................ 8
3. Set Column Alias Names .......................................................................................................................................... 10
Alias Columns........................................................................................................................................................... 11
4. User Interface & Attribute Map ............................................................................................................................... 12
Attribute Map .......................................................................................................................................................... 12
RHS Toolbars ............................................................................................................................................................ 13
5. Select Variables ........................................................................................................................................................ 14
6. Validate Data ........................................................................................................................................................... 16
7. Display Data in Tabular View ................................................................................................................................... 18
8. Display Data in Plot Window ................................................................................................................................... 19
Zooming and Panning .............................................................................................................................................. 19
View Data Labels ...................................................................................................................................................... 20
9. Open Multiple Plot Windows................................................................................................................................... 22
Scatterplots .............................................................................................................................................................. 22
Probability Plots ....................................................................................................................................................... 22
Histograms ............................................................................................................................................................... 22
10. Apply Colour/Shape/Size Attributes ...................................................................................................................... 24
Auto-Attribute Text Data ......................................................................................................................................... 24
Show Legend ............................................................................................................................................................ 25
Change Visibility....................................................................................................................................................... 26
Auto-Attribute Numeric Data .................................................................................................................................. 27
11. Make Data Selections ............................................................................................................................................ 30
12. Univariate Statistics ............................................................................................................................................... 33
Summary Statistics .................................................................................................................................................. 33
Frequency Table ...................................................................................................................................................... 34
Correlation Matrix ................................................................................................................................................... 34
13. Ranked Variable Maps and Gridding ..................................................................................................................... 35
Ranked Variable Maps ............................................................................................................................................. 35
Gridding ................................................................................................................................................................... 36
14. Display Data in Classification Diagram ................................................................................................................... 38
15. Additional Features................................................................................................................................................ 40
Page 3 of 48
Scatterplot Matrix (SPLOM) ..................................................................................................................................... 40
Point Density Gridding and Mineral Nodes ............................................................................................................. 41
Calculations Menu ................................................................................................................................................... 41
Multivariate Analysis Tools ...................................................................................................................................... 41
Generate Classification Diagrams ............................................................................................................................ 42
16. Copy, Save and Print Options ................................................................................................................................ 43
Save Checkpoint ...................................................................................................................................................... 43
Save ioGAS File ........................................................................................................................................................ 43
Save As ioGAS File .................................................................................................................................................... 43
Copy Window as Image ........................................................................................................................................... 43
Copy Graph as Image or Vector File ........................................................................................................................ 43
Save Graph as Vector File ........................................................................................................................................ 44
Print Graph .............................................................................................................................................................. 44
17. Export and GIS Options .......................................................................................................................................... 45
Export Data .............................................................................................................................................................. 45
Export to Google Earth ............................................................................................................................................ 45
Export to ArcGIS ....................................................................................................................................................... 46
Export to MapInfo ................................................................................................................................................... 46
ioGAS Link for GOCAD.............................................................................................................................................. 47
ioGAS Link for Leapfrog Geo .................................................................................................................................... 47
Help System ............................................................................................................................................................. 48
Training Videos ........................................................................................................................................................ 48
Frequently Asked Questions .................................................................................................................................... 48
Technical Support .................................................................................................................................................... 48
Page 4 of 48
Quick Start Tutorial Overview
An ioGAS evaluation licence is valid for two weeks* and the software is fully functional during this time. After this time the software can only be used with a valid licence file.
To learn how the ioGAS program works we recommend viewing the Getting Started With ioGAS video. This is a detailed video that covers many of the features of ioGAS and how they work.
Use the steps in this tutorial to follow a typical workflow to get you up and running and using various features of the ioGAS software. The tutorial uses an excel version of the ioGAS demonstration dataset.
For our maintained users there are a number of additional training videos available from the Help>Training Videos menu.
Contact [email protected] to purchase ioGAS or for any other enquiries.
* The two week trial period is not available for MAC installations. If you are running a MAC computer please install ioGAS and then start the program. Click on the Send Machine ID button in the displayed message and copy/paste the Machine ID number into an email and send to [email protected] to obtain an evaluation licence file.
Page 5 of 48
1. Import Data
ioGAS can support the following file types:
ioGAS files (.gas files)
Tab-delimited text files (.txt files)
Comma-delimited text files (.csv files)
Excel Spreadsheet files - all (.xls, .xlsx files)
XRF Files - Olympus Innov-X (.dbf, .csv files), Niton (.ntg files)
MapInfo GIS files (.tab files)
Geography Markup Language files (.gml, .xml files)
Data from external databases - see File>Open Database menu option:
ODBC Database (Access, SQL, etc)
REFLEX HUB Data
ALS Webtrieve
Open Excel File
1. Select File>Open. or click on the Open File icon on the Main Toolbar.
2. Browse to one of the following locations depending on what operating system is installed:
PC users (32-bit OS): C:\Program Files\ioAnalytics\ioGAS\demo data folder
PC users (64-bit OS): C:\Program Files\ioAnalytics\ioGAS-64\demodata folder (or C:\Program Files (x86)\ioAnalytics\ioGAS\demodata folder if 32-bit version of ioGAS is installed)
MAC users: ioGAS Application\Contents\Resources\app\demodata folder
3. Use the drop-down arrow next to Files of type: and select Excel Spreadsheet files - all (.xls, .xlsx files). Highlight the Demo.xlsx file and click on the Open File button.
Page 6 of 48
Page 7 of 48
2. Define Column Types
Generally when a dataset is first imported into ioGAS the Column Properties dialog is displayed. This is where columns in the dataset are matched to columns required by ioGAS in order for data to be plotted successfully.
Column Properties dialog showing assigned special columns
Special Columns
This section is where the sample number and coordinate columns in the dataset are selected so they can used to display data in the plot windows.
ID - Unique sample identifier.
East/North - X and Y coordinate columns. Used to display data in all spatial map views. Generally these will be in a projected coordinate system such as UTM coordinates.
Page 8 of 48
East/North Projection - Coordinate system used for East/North columns above. This is the projection that is used in the geographical file exports, eg. gridded images as GeoTiff Images or ER Mapper grids, ArcGIS and MapInfo exports
Elevation - Z value column. Required to display data in 3D spatial Plots.
WGS84 Longitude/Latitude (decimal degrees) - Separate X and Y lat/long coordinate columns in WGS84 decimal degrees required in order to export data to Google Earth.
1. Match the columns in the demo dataset to the following Special Columns in ioGAS:
ID = Sample Num
East = East_AMG84_z51
North = North_AMG84_z51
East/North projection = AMG (AGD84) Zone 51
WGS84 Longitude (decimal degrees) = Long_WGS84
WGS84 latitude (decimal degrees) = Lat_WGS84
Column Name and Type
Underneath in the Column Name and Type area ioGAS automatically assigns each column in the dataset as either Numeric, Text or Non-Plot. Sample ID and coordinate columns listed above are assigned as Non-Plot, ie. not variable columns.
Variable columns are assigned as numeric or text. Analysis data to be used in plots is generally numeric whereas text data is used to 'group' data, for example Regolith Unit, Geology, Sample Medium, etc. If a column is imported as a text field yet contains numeric data then the column can be re-assigned as a numeric column and vice versa.
2. Scroll down and have a look at the different column types assigned to this dataset
Non-Plot columns have a grey circle next to them while text columns have a black circle. Numeric columns can have either a blue circle or a green circle next to them depending on whether they are "aliased" or not. See Step 4 for more information on aliasing variables. Red circles denote that there is a problem such as duplicate column names and will need to be fixed before exiting this dialog.
ioGAS lists the number of samples in each column that are numeric, text or null (blank) on the right-hand side of the dialog. There are 999 records in the demo dataset.
3. Place the cursor over the original column name (without mouse clicking) to view tooltip information about the data in the selected column. Text columns display the individual categories and numeric columns display min, median and max values. If the tooltips do not appear click within the window to make it active and try again.
Page 9 of 48
Note that it is still possible to plot data and use many of the functions within ioGAS without having an ID column selected. This is true for spatial fields as well and it is possible to set any of these at any time.
4. It is also possible to remove any columns before import by clicking on the cross next to the column to delete. These columns will be permanently removed from the imported dataset when the OK button is selected.
See Column Properties in the Help>Help menu for more information.
Page 10 of 48
3. Set Column Alias Names
One very important feature of ioGAS is that if the element and the units that the values are captured in is known for each column, ioGAS can perform unit or element/oxide conversions on-the-fly in order to use the data with the classification diagrams, calculations and spider plot normalisations shipped with the program if the data is not already in the required format.
Column Properties dialog showing list of element/unit combinations to select for column aliasing
The way to "alias" columns is to select a standard geochemical element/unit combination from the Alias pull-down list next to each variable. When a column is "aliased" the circle next to this column is then coloured green, (indicating that it is a numeric column that is aliased) rather than blue (numeric) or black (text) as shown in the screen capture above.
Observe the original names in the demonstration dataset compared with their "aliased" names that include what units they are captured in. If ioGAS can already guess the "aliased" name from the original
Page 11 of 48
column name it will attempt to automatically assign an "aliased" name when the file is imported. Eg. Au_ppb
Note: In ioGAS all variables can be renamed as desired and the new name will be shown everywhere in the program. To enter a new name for a column simply overwrite the one displayed in the Alias column for that variable.
Alias Columns
Use the following steps to "alias" the columns in the demonstration dataset to standard element/unit names:
1. Click on the Guess Aliases button. ioGAS will automatically guess the element and unit from the original column name for all columns. To alias a single column at a
time use the Guess Alias button next to each variable.
2. It is important to check the data to make sure that the correct element/oxide/unit combination
name has been applied. To manually assign an alias name to a column select the appropriate element/oxide/unit combination from the Alias pull-down list. To reset a single column back to
the original name click on the Reset Alias button next to each column or reset them all
using the Reset Aliases button.
3. When you are satisfied that the columns have been "aliased" correctly click OK to proceed.
The Column Properties settings are retained when the file is saved in ioGAS format and can be modified
at any time by clicking on the icon on the Main Toolbar. Note that all open plot windows will be closed when you do this.
See Alias Columns for more information.
Page 12 of 48
4. User Interface & Attribute Map
The imported dataset is now loaded into ioGAS with the file name and path displayed in the titlebar of the program.
In the middle of the screen is the Attribute Manager window. The Attribute Manager is used to control the way data points appear in plot windows. It is used to apply colour, shape and size attributes and turn on/off the visibility for different groups of data. We will look at how to create and change attributes in Step 10 of this tutorial.
At the top of the screen are a series of pull-down menus with the Main Toolbar displayed underneath. Many functions are replicated in both the menus and the Main Toolbar and some functions also have keyboard shortcuts, eg. Open File (Ctrl + O). shortcuts are displayed next to the menu items.
A status bar is present at the bottom of the screen. Information about objects in plot windows or data warnings are displayed here.
Attribute Map
An Attribute Map is a pseudo-map or geographical view of a dataset that plots the X coordinates against the Y coordinates. It is used to view a dataset in a spatial context and is one of the main plot types which is exported to Google Earth or GIS programs such as ArcGIS or MapInfo.
Page 13 of 48
1. Click on the Display Attribute Map icon on the main toolbar.
Attribute map window with RHS toolbar icons
RHS Toolbars
When the Attribute Map is open, a number of buttons are displayed vertically on the right-hand side of the screen. This toolbar is referred to as the RHS (or ight-Hand Side) Toolbar and will contain different buttons depending on the active plot window. To make the RHS toolbar active simply click in the plot window or on the window titlebar that you want to work with. Place the cursor over each icon to view a tooltip description for each icon on the RHS toolbar.
To move the Attribute Map window click on the window titlebar and drag to a new location while holding down the left-mouse button. Plot and other windows that are opened into ioGAS can be re-sized by placing the cursor over one of the edges of the window and then dragging it in or out. Minimise,
Restore and Close buttons are also available in the top right hand corner of each open window.
Page 14 of 48
5. Select Variables
Before any data can be displayed in a plot window (aside from an Attribute Map if coordinates are present) the variable columns must be selected for use. The current variable selection is generally shown in the main window title after the file name, which in this case is empty as there are no variables selected yet.
Notice that a number of icons are greyed out on the main Toolbar. This also indicates that either no variables are selected for use or that not enough variables are selected to display that particular plot, e.g. a ternary plot requires three variables to be selected before the icon will be active.
1. To select variables go to Data>Select Variables or click on the icon on the Main Toolbar.
Select Variables dialog with four selected variables
Provided - Groups of commonly used elements provided by ioGAS. Individual variables can be added or removed from these selections. Provided groups include:
Element Groups - Majors , Immobile, REE, PGM
Deposit Style - Porphyry Cu-Au, Epithermal/Mesothermal/Orogenic/Laterite Au, IOGC, MVT, VHMS, plus many more.
Secondary Scavenging - Fe and Mn Oxides
Goldschmidt - Chalcophile, Lithophile, Siderophile
Page 15 of 48
History - Each variable selection is saved and is available to be selected for use again with the current dataset from this pull-down list.
2. Add the following variables to the Selected Window: Zn_ppm, Ni_ppm, Fe2O3_pct and Cu_ppm.To select an individual variable double-click on the entry in the Available window to move it across to the Selected window or use the arrows in the middle of the dialog. Multiple selections can be made using the Ctrl/Shift keys.
Note that the colour of the variable columns match the colours used in the Column Properties dialog. As all the selected variables are green they are numeric columns which have been "aliased" to the standard ioGAS element/unit names. The black variables are text fields and can be selected for use with plots if they will produce meaningful results. Numeric variables which have not been aliased will appear in blue.
The order of the variables in the Selected window can be modified using the Up and Down arrows or by dragging to a new location with the mouse cursor. For some plots such as XY Scatterplots the first variable is used as the X axis when there are multiple variables to be plotted. Ternary plots use only the first three variables in the Selected window so re-ordering is often required to ensure the correct variables are displayed.
2. Click OK to exit the dialog.
Note if some of the main toolbar icons are still greyed out even when variables are selected this may indicate that there are not enough variables selected to be used with that feature. Eg. a ternary plot requires three selected variables before the icon will be active.
The current variable selection is now shown in the main window title after the open file name.
See Select Variables for more information.
Page 16 of 48
6. Validate Data
1. Open the Validate menu and have a look at the options available to validate data. These include:
Data Doctor - The Data Doctor tool displays the number of null, 0, -, > and < records for each of the selected variables. Using this tool It is possible to replace below detection limit values with a ½ positive value or custom value and above detection values with a custom value. Colour attribute any of these samples in open plot windows to see where they are located. Any changes made to the data are recorded in a log file for future reference.
Search and Replace - Replace text or numeric entries in selected columns or the entire dataset. All modifications reported in the log file.
Converting Zeroes to Null (Non-Plot Columns) - Replace zero entries in non-plot or coordinates columns with null values. This is useful when there are 0 values in coordinate columns that plot at 0,0 in map views.
2. Select the Validate> Data Doctor option.
The Zn_ppm and Cu_ppm columns contain some below detection limit data. The validation type, the value, the number of samples with this value and the % of affected valid data is displayed along with a recommended replacement value which in this case is 1 (the half positive value of the below detection limit, i.e. -2).
3. Check the Replace Value box next to each entry and then click Apply.
As the replacements are made the updated Data Doctor reports that there are now no data validation problems with the dataset.
Page 17 of 48
4. Click on the Show Log button at the bottom. In the Change Log window scroll to the right to view the number of Zn_ppm and Cu_ppm occurrences that have been updated with the new replacement value.
The Change Log file lists all changes to a dataset from when it is first imported into ioGAS and records all data validation replacements, columns removed and rows deleted. See Data Doctor for more information on how to validate your data with this dialog. The Change Log can be accessed at any time using the Data>Show Change Log menu option.
5. Select Close to exit this window and then Close to exit the Data Doctor window.
See Validate for more information on other menu options.
Page 18 of 48
7. Display Data in Tabular View
The View Data tools displays the dataset in a spreadsheet or tabular view as rows/columns.
1. Select Data>View Data (All Columns) or click on the icon on the Main Toolbar. This will display all the columns in the dataset regardless of what variables are selected.
2. Click on the Maximise button in the middle of the buttons in the top right of the Data window to make the window bigger.
3. Use the scroll-bars to scroll up and down and left and right to get a feel for the columns in the dataset. Note the colour, shape, size and visible columns that are showing the current attributes that are applied to each data row. These are currently set to the default attributes.
4. Sort a variable column in ascending order by left-mouse clicking once in the column header. Click again in the header to reverse the sort. The [Order] column is automatically generated when the data is imported and can be used to sort the data back to its original import order at any time.
5. It is possible to click on rows in this view and apply colour/shape/size attributes to the selection using the Apply Attributes to Selection button. This will be covered later in this tutorial. Data can also be copied into other programs using the two Copy buttons at the bottom of the dialog.
6. Close the Data window using the X in the top right hand corner.
See Display Data in Tabular View for more information.
Page 19 of 48
8. Display Data in Plot Window
1. Go back to the Attribute Map that we created earlier. If you need to re-open this plot select the
Map>Attribute Map menu option or click on the icon on the Main Toolbar. If the RHS toolbar is not displayed click on the titlebar of the Attribute Map window. Maximise the window to make it easier to see.
On the RHS Toolbar there are a number of standard tools available to move about within a plot window and we will have a look at some of these now.
Zooming and Panning
2. To zoom in on an area click on the icon and drag a box in the window over some data points using the left-mouse button. The window contents are zoomed to the extents of this box. Alternatively, place the cursor in the plot window and use the scroll bar on your mouse to zoom in and out at the cursor location.
3. Click on the icon and click and drag the left-mouse button in the plot window to pan the view.
4. Right-mouse click in the window and select Zoom Previous from the pop-up menu. To restore the data to the original extents select Zoom to Data.
Page 20 of 48
5. You can also use the Dynamic Zoom tool to zoom in and out by holding down the left-mouse button in the plot window and then dragging it up to zoom out or down to zoom in. Note that you can also use the scroll bar on the mouse to zoom in and out if available. Restore the plot view when you are finished.
View Data Labels
6. Place the cursor over a data point in the plot window (without clicking) until a tooltip information
box is displayed. The information displayed in this box includes the ID, East and North coordinates, any colour/shape/size attribute groups which are assigned and any columns selected to be displayed as labels. e.g. Regolith and Geology units to which the sample belongs.
7. Select the Data>Select Labels menu option. This is where it is possible to choose which other columns will display in the tooltip information box.
Select the Regolith and Geology columns and a couple of other variables and move them into the Selected window. Click OK.
Click back in Attribute Map window to make it active and place the cursor over a sample. The new label columns are now displayed.
Page 21 of 48
See Attribute Map for more information.
Page 22 of 48
9. Open Multiple Plot Windows
Now we will open some other plots that are available in ioGAS and look at some of the different ways in which they can be displayed.
Scatterplots
1. Select Graph>XY Plots or click on the icon on the main Toolbar.
See that only three XY plots are created. This is because although we have four variables selected: Zn_ppm, Ni_ppm, Fe2O3_pct and Cu_ppm, the Zn_ppm column is used as the X axis in all three cases and the other variables as the Y axis.
2. With the XY Plot window as the active window, select the Log X Axis and Log Y Axis icons from the RHS toolbar. Clicking on these icons will change the X and Y axes from raw data values to a Log scale.
3. If you click on each of the or icons the X and Y axes will change to a Power Transformed axis. ioGAS uses a Lambda power transformation method to de-skew data so it more closely approximates a normal distribution. Click on the Power buttons axis icons again to return to the raw data value axes.
See Scatterplot toolbar for information on the other features available to display on these plots.
Probability Plots
4. To create a probability plot for each variable select Graph>Probability Plot or click on the icon on the main Toolbar. This time each variable is displayed in a single plot window. It is possible to zoom, pan and log/power transform the Y axis from the RHS Toolbar.
Use the icon to display probability values along the X axis instead of N-Score (std dev) values.
Use the icon to change the distribution to show a cumulative frequency plot. See Probability Plot toolbar for more information.
5. Select Window>Tabbed Window. A circle is placed next to this menu entry to show this window mode is selected.
Histograms
6. Select Graph>histograms or click on the icon on the main Toolbar. See that each of the variable histograms is displayed in a separate tab in the same window. If we had not selected Tabbed Windows prior to creating the histograms they would have all been displayed in the same plot window like the probability plots. The histograms show the number of samples in each
Page 23 of 48
binning range. Binning ranges can be increased or decreased using the and arrows on the RHS Toolbar.
7. We now have four plot windows open but they are most likely all sitting on top of each other. To arrange multiple windows go to the Window menu. Click on the Cascade Windows option to view all the windows with their titlebars visible. Then select the Window>Tile Windows option to view all the plot windows without overlapping.
8. Select Windows>Normal Windows again to return to the default window display. Note that this is applied to all windows opened from now on, not those already open.
See Create Graphs for more information.
Page 24 of 48
10. Apply Colour/Shape/Size Attributes
Now that we have some plot windows created we will look at how to change the colour, shape and size attributes for individual data points, apply them to data selections and turn the visibility of data points on and off. This is all controlled by the Attribute Manager.
Auto-Attribute Text Data
Auto-Attributing can be used to apply attributes to data based on unique values in a text column or data percentiles/custom ranges for numeric columns.
1. To display the Attribute Manager select Graph>Display Attribute Manager or click on the icon. You can also use Ctrl-A as a keyboard shortcut to open the Attribute Manager window. This window can be dragged outside of the application if you are running dual screens to save you having to open it up all the time.
Alternatively, select Window>External Windows Always on Top to keep the Attribute Manger window displayed on top of other plot windows instead of minimising.
The Attribute Manager contains three tabs, one each for colour, shape and size.
2. Leave Regolith Unit as the selected column and click on the Auto-Attribute button. This will colour the data points according to which regolith unit they are assigned. The Attribute Manager also lists the number of data points in each colour category and how many of them are currently visible (note it is possible for samples to be marked as not visible on other attribute tabs).
The data is now coloured by Regolith Unit in every plot window.
Page 25 of 48
3. Click on the Shape tab this time. Select Geology from the column pull-down list. Click on the Auto-Attribute button. The data points are now coloured by regolith unit and their shape represents the underlying geological unit.
Show Legend
4. Click on the Legend icon on the main toolbar to open up a separate legend window. To view the attributes in a combined legend, right-mouse click within the legend window and choose Legend Mode - Combined/Separate. Click this option again to return the default legend view.
Page 26 of 48
Change Visibility
Back in the Attribute Manager, if we want to sub-set our data so that we are only looking at data points from particular regolith units we can turn off the visibility for those groups we do not want to see.
5. Uncheck the box in the Visible column next to the D9 and DA regolith groups in the Colour tab. The rows visible column is set to 0 for the selected groups.
Observe how the data points are removed from all open plot windows.
Page 27 of 48
6. Check the boxes to re-display the samples or click on the All Visible button at the bottom of the Attribute Manager.
Auto-Attribute Numeric Data
7. While still in the Colour Tab select a numeric variable column such as Cu_ppm from the column pull-down list.
8. For numeric data columns, data points are attributed according to a selected percentile binning range, eg. 5 or 10 equal ranges, Quartile, Progressive, etc and then coloured using one of the supplied colour ramps. Click on the down arrow next to 5 Equal Ranges and select Progressive from the binning range pull-down list. The Progressive binning range divides the data into percentiles based on 30, 60, 80, 90, 95 and 98% cut-offs.
9. Click on the arrow next to the colour ramp and look at the available options. For the purposes of this exercise we will use the default ioGeochem Linear colour ramp at the top of the list.
10. Click Auto-Attribute to apply the colours and select "YES" to overwrite the existing ones.
Page 28 of 48
11. Observe how the values are updated in the legend.
12. Experiment with Auto-Attributing data using different text columns and also with numeric columns using different colour ramp/binning combinations.
13. To change the assigned colour/shape/size of an attribute double-click on the attribute (eg. red circle, square, etc) and select a different one from the colour palette or drop down list (for shape/size). It is also possible to change the name of an attribute by double-clicking in the Name column and overwriting the entry with a new one. Note any changes will be displayed in the legend window but will not be written back to the dataset.
Page 29 of 48
12. Highlight the PEw entry in the Shape Tab. To remove this entry from the list use the
button. All of the PEw samples now show the Default Shape. To remove all
the Shape attribute entries click on the button.
13. To remove all the currently applied colour/shape and size attributes click on the
button.
It is possible to attribute data by applying the same variable to the colour, shape and size attribute tab or apply three different variables. It is also possible to create custom bin ranges rather than percentiles which can be applied to different datasets. See Create and Edit Bin Ranges for more information on how to do this.
See Attribute Data using Column Values for more information.
Page 30 of 48
11. Make Data Selections
The Attribute Manager can also be used to assign colours, symbols or different sizes to manually selected data points in a plot window.
1. Remove all existing attributes using the Global button in the Attribute Manager.
2. Select the Colour tab and click on the Add an Attribute button. A New Colour row is added under the default colour row and is coloured red.
3. Double-click on the New Colour entry to assign a name for the attribute (ie. High Cu) and then click Enter. Click on the red colour circle to select a different colour if desired. Make sure that the High Cu row is highlighted (in blue) and that a red circle with "High Cu" is also displayed in the top right of the Attribute Manager window.
4. Select the Shape tab and click on the Add an Attribute button three times. See how each new row has a different shape in it. Click on the Triangle row so it is highlighted in blue. Repeat this process in the Size tab and click on the 10 row.
5. The shape and size attributes should display in the top right corner as "New Shape" and "New Size" when they are highlighted correctly.
6. Click in the Probability Plot window created in Step 9. Otherwise click on the Probability Plot icon on the main toolbar again if the plot window has been closed. Re-size this window to make it bigger and make sure the Probability Plot RHS Toolbar is visible by clicking in the plot window.
7. Select the Attribute Polygon icon from the right-hand side toolbar.
Page 31 of 48
8. In the Cu_ppm probability plot window hold down the left mouse button and click around the high values in the plot window to create a polygon (region) object. Double-click to finish. All of the data points within the polygon should now be attributed with a red triangle 10 pt in size.
9. Select Windows>Tile Windows again to view all the open plot windows. Note that the selected points are attributed in the other plot windows and if you open up the legend window it has also been updated.
10. Leave the High Cu samples attributed and repeat the process outlined in steps 2-8 to make another selection on the probability plot using a blue square 10 pt combination. Make sure that blue colour, square shape and Size 10 pt attributes are highlighted in their respective tabs and displayed in the Attribute Manager top right corner prior to making the data selection.
Page 32 of 48
10. This time, zoom in on the probability plot and select individual points to attribute using the
Attribute Point icon.
12. Use Data>View Data (All Columns) or click on the icon on the main toolbar to open a tabular view of the data and note the colour, shape and size attributes have been updated next to each row. To see this more easily left-mouse click in the [Colour] column header cell twice to display the data in descending order based on colour.
13. To save a selection as a new column select use the Make Variable from..... options from the Data menu.
14. Open the Attribute Manager again if it has closed and remove all attributes using the Global button and experiment with creating different colour, shape and size attribute combinations and applying them to data selections. Note that the selections can be made in most plot windows.
15. Close all plots at the completion of this exercise using Windows>Close All Windows.
See Make Selections and Apply Attributes for more information.
Page 33 of 48
12. Univariate Statistics
Summary Statistics
When analysing data it is useful to look at various statistical parameters for either the entire dataset or for selected categories within a dataset. The selected categories are based on the colour groups as set in the Attribute Manager.
1. Open up an Attribute Map (Graph>Attribute Map) or click on the icon.
2. Open the Attribute Manager using Ctrl-A and colour Auto-Attribute the data using the Regolith unit column. See Step 10.
3. Select Analysis>Display Summary Statistics or click on the icon on the main toolbar.
In the Summary Statistics window all of the selected variables are displayed along with a number of basic statistics for each regolith group. The values in each group are also coloured according the colours in the Attribute Manager. The values at the top in black are the calculated statistics for all visible data regardless of colour group as denoted in the Attribute Manager.
4. To change the displayed statistics click on the icon on the RHS Toolbar. Check or uncheck the statistics as required and click Apply to update.
5. Click on the Change Grouping icon on the RHS Toolbar to group the data by statistic rather than by group.
6. Close the Statistics window and the Choose Statistics dialog using the X in the top left hand corner when complete.
Page 34 of 48
See Summary Statistics for more information.
Frequency Table
View all the unique values for each selected variable and the counts for each using a Frequency Table.
1. Select Analysis>Display Frequency Table.
Each variable is displayed in a separate tab.
Correlation Matrix
Display the correlation coefficient values for each paired combination of selected variables.
1. Select Analysis>Display Correlation Matrix.
Highly positive or negative correlated pairs of data are coloured in pink and red.
Page 35 of 48
13. Ranked Variable Maps and Gridding
Ranked Variable Maps
A Ranked Variable Map displays each of the selected variables in a separate map view. The data points in each map are ranked and then displayed using one of the pre-defined colour and size ramping options. Ranked variable maps are good for comparing high or low concentrations across multiple elements.
1. Select Window>Normal Windows menu option if it is not already selected.
2. Select Map>Ranked Variable Maps or click on the icon.
3. To view what data values are represented by their colour and size attributes click on the
Show/Hide Colour .Bar Legend icon on the RHS toolbar.
4. To modify the thematic settings click on the icon on the RHS (Right-Hand Side) Toolbar. Select from a number of different Colour and Size ramps and observe how the data appearance changes. To see what type of size ramp is being applied place the cursor over the entry in the pull-down list. Repeat for the colour ramps.
5. Ranked variable maps can be exported and viewed in Google Earth, ArcGIS and MapInfo.
See Ranked Variable Maps for more information.
Page 36 of 48
Gridding
A grid is created from the interpolation of located data onto a regular grid or matrix that is then rendered so that it can be viewed as a continuous coloured or shaded surface. ioGAS includes a gridding tool that uses a modified Inverse Distance Weighting algorithm to generate the interpolated grid cell values.
Grids created for selected variables using default settings
1. Select Map>Gridding or click on the icon.
2. The Make Grids dialog is displayed.
Page 37 of 48
ioGAS attempts to automatically select the appropriate grid cell size settings for the dataset based on an algorithm that analyses the spatial structure of the data. All of the other gridding parameters including grid cell size, search radius, smoothing, etc can be customised.
3. Leave the default settings and click OK. The grids are displayed in a single plot window.
4. To view what grid cell values the colours represent click on the Show/Hide Grid Legend icon on the RHS toolbar.
5. Overlay the attribute points on top of the grid using the icon.
6. Place the cursor over the grid and use the zoom tools (or mouse scroll bar) to zoom all the grids together at the cursor location.
7. To change the grid parameters select the Display Grid Options icon from the RHS toolbar.
The gridded images can be exported using the GeoTiff and ER Mapper Grid export options on the RHS Toolbar.
See Gridded Images for more information.
Page 38 of 48
14. Display Data in Classification Diagram
ioGAS contains a number of standard classification diagrams arranged into a logical menu system. Data can be plotted on classification diagrams and then attributed according to the classification group in which they are located. These attributes can be written back to the file and used in further analysis or exported for use in third party programs.
In order to view data on a supplied classification diagram the variable columns must be "aliased" in the Column Properties dialog as outlined in Step 3. This is so ioGAS can perform any element/oxide/unit conversions to get the data into the correct format to display on the diagram.
In this exercise we will display the demonstration dataset on a Regolith diagram that plots K/Al vs Mg/Al wt values to classify regolith data into transported clays, saprolite and younger alluvium/coluvium.
1. Select Diagram>Provided>Regolith>Classification>Regolith Fractionation (McQueen, 2006)
2. The data are plotted with the current attributes onto the diagram in a new plot window. The diagram window contains zooming, panning and selection tools the same as we have observed in other plots. If you zoom out you can see that not all the data plots within the diagram extents.
3. Right-mouse click and select Zoom to Diagram from the pop-up menu to return to the original diagram view.
4. To attribute the data points with the regolith classification group colours select the Colour Rows
from Polygon icon on the RHS Toolbar and select "YES" to overwrite existing colour attributes.
Page 39 of 48
5. To make a new variable column which contains the regolith classification group for each row select Data>Make Variable from Colour menu option.
6. Change the new column name to "Regolith Classification - McQueen" and when the column is
created open up a tabular view of the data (View Data icon on the main Toolbar) and scroll to the right to see the newly added columns.
One column is text with the rock classification based on the polygon name, the other column is numeric with a different number for each rock classification. Note that data that falls outside of the diagram polygons is assigned the default black colour and a numeric value of 0. All other samples are assigned their regolith classification group.
It is possible to make and edit your own classification diagrams and share them with others within your organisation. See Classification Diagrams for more information.
Page 40 of 48
15. Additional Features
Scatterplot Matrix (SPLOM)
A scatterplot matrix is a good way to look at the correlation between multiple variables at the same time. An XY plot of each variable pair is displayed separately by a probability plot for individual variables.
1. Close all currently open windows using Window>Close All Windows and remove any attributes by clicking on the Global button in the Attribute Manager.
2. Select Data>Select Variables or click on the icon on the Main Toolbar.
3. Highlight all the variables in the Selected window and then click on the Unselect All button to remove them from view.
4. Choose SiO2_pct, TiO2_pct, Al2O3_pct and Na2O_pct and move them to the Select window. Click OK to exit this dialog.
5. Select Graph>Scatterplot Matrix or click on the icon on the main Toolbar.
6. Open the Attribute Manager and colour the data points by Regolith (See Step 10)
Scatterplot Matrix showing XY plots for all paired variables and correlation coefficient values
Page 41 of 48
7. Use the RHS toolbar icons and to show the mean and median locations with respect to the data. Click each button three times to cycle through showing the mean or median of each regolith unit with data points and without the data points. The grey crosses denote the mean or median sample location for all visible data points regardless of regolith unit.
8. Use the and icons to display a Y=X line in each XY plot and regression lines by colour group and for all visible data. Cycle through the options to see how they work.
Point Density Gridding and Mineral Nodes
9. Click on the Point Density icon on the RHS toolbar. Point density grids help to focus on areas where the bulk of the data are located. Click on the point density icon to cycle through the
different opacity levels. To change the grid options use the icon.
10. Right-mouse click on the Al2O3_pct : SiO2_pct (-0.61) plot and select the XY Plot [Al2O3_pct : SiO2_pct] option at the bottom of the menu. This will open up this XY plot into a separate window. Zoom out to make some more room around the point density grid.
11. Click on the icon on the RHS toolbar. A number of mineral nodes with abbreviated names are added to the XY plot. Click on the icon to cycle through showing the mineral nodes with a line to origin, full mineral names and then the mineral formulae.
12. Click on the icon. In here is a list of all the available mineral and rock nodes. Select the All Off button and click on the Sheet Silicates tab. Select Group On and view the nodes in the plot window. To return to the default settings click on the Reset button. Close dialog upon completion.
Experiment with other plots available in ioGAS including 3D Plot, Spatial 3D Plots for drillhole data, Line Plot, Parallel Coordinate Plots, Spider Plots, Box Plots and Pie Charts.
Calculations Menu
Create your own Calculated columns or select from one of the Quick Calculation options: log 10, z-Score and mean/median transformations and molar calculations. Otherwise use a calculation from the Provided library. Calculated columns can also be used as axes in the creation of classification diagrams.
Multivariate Analysis Tools
Principal Components Analysis
Mahalanobis Distance Calculations
Page 42 of 48
RGB Classification
Simple/Multiple Regression Analysis
Cluster Analysis
Discriminant Projection Analysis
Generate Classification Diagrams
Create your own Classification Diagrams and use them with different datasets.
Page 43 of 48
16. Copy, Save and Print Options
Save Checkpoint
When working in ioGAS it is possible to save a snap-shot of a session at any time using the File>New Checkpoint menu option.
When this menu option is selected all open windows and the currently assigned colour/shape/size and visibility attributes are saved. It is then possible at any time in the future to restore ioGAS to one of these saved checkpoint states by selecting it from the Checkpoint list. See Save and Restore Checkpoints for more information.
Save ioGAS File
1. Select File>Save or click on the icon.
The Save option saves both the current data and the attribute information as a native ioGAS file. Any open plot windows are also saved and will be re-opened when the file is next loaded. To re-open a native ioGAS file use the File>Open menu option.
Save As ioGAS File
To save a copy of an ioGAS file select File>Save As and choose ioGAS File from the Files of Type pull-down list.
NOTE: The Demo file is Read-Only so cannot be saved with new changes. To make an editable copy of this data use File>Save As and save using a new name.
Copy Window as Image
This option creates a bitmap image of the active window and copies it to the clipboard.
1. Select Edit>Copy or click on the icon on the main toolbar.
2. Paste into a third party program such as Word, Powerpoint or image processing package using "Paste" or Ctrl-V.
Selected plots such as Scatterplots, scatterplot matrix, ranked variable maps and line plots have a copy
button on the RHS toolbar that will copy the window at high resolution for large scale plotting, eg. at A1 or A0 size.
Copy Graph as Image or Vector File
1. Right-mouse click in a graph window and select from one of the following Copy options. The Bitmap copy has a number of screen resolutions. The larger the resolution the larger the resulting image which is created.
2. Paste into third party program such as Word, Powerpoint or image processing package using "Paste" or Ctrl-V.
Page 44 of 48
It is also possible to copy windows in EMF (Enhanced Metafile format) and EPS (Encapsulated Post Script format). These are both vector based file formats that enable the image to be re-sized while retaining resolution and editing of the individual map components in other programs such as Corel Draw, Paint Shop, Powerpoint and Word.
Save Graph as Vector File
1. Right-mouse click in the graph window and select from one of the following Save options.
2. Enter a name and location for the saved file.
The EPS (Encapsulated Post Script), EMF (Enhanced Metafile) and SVG (Scalable Vector Graphics) are all vector based file formats that enable the image to be re-sized while retaining resolution and editing of the individual map components in other programs such as Corel Draw, Paint Shop, Powerpoint and Word.
Print Graph
To print an individual graph directly from a plot window right-mouse click and select Print from the pop-up menu.
See Save, Export, Copy and Print Options for more information.
Page 45 of 48
17. Export and GIS Options
Export Data
1. Select File>Export (All Rows) or File>Export (Visible Rows)
ioGAS can export data in the following formats:
Excel Spreadsheet File
CSV Text File
Tab Separated Text File
GML (Geography Markup Language) File
Google Earth KMZ File (as Attribute Map)
AutoCad DXF File
All Rows will export all the rows in the dataset whereas Visible Rows will only export data that is set as visible in the Attribute Manager. The Visible Row export option is good to use when you need to sub-set data into a separate file.
The File>Export Selected Columns menu option will export only the columns flagged as special in the Column Properties dialog plus the columns selected in the Select Variables dialog. Options to export all rows and visible rows are also available.
Export to Google Earth
1. Select Map>Export to Google Earth or click on the icon on the Attribute Map or Ranked Variable Map RHS (Right-Hand Side) Toolbar.
To export into Google Earth the dataset must contain coordinates for each data point in Lat/Long WGS84 projection and these columns must be selected as the 'WGS84 Longitude' and 'WGS84 Latitude' columns in the Column Properties dialog (see Step 3).
When the Attribute Map is exported to Google Earth, the shape, colour and size attributes will be rendered correctly. Ranked Variable Maps can also be exported into Google Earth, and like in ioGAS the colour and size are in proportion to the rank.
Page 46 of 48
Google Earth KMZ export showing data points and attributes
See Export to Google Earth for more information.
Export to ArcGIS
This option will save an Attribute Map including any colour, shape, size and visibility attributes and export them to an ESRI geodatabase with an associated Layer file.
The Export to ArcGIS utility can only be run using the ioGAS 32-bit version with at least ArcGIS version 10, SP 2 installed.
1. In the Column Properties dialog make sure that the East/North Projection is selected to match the coordinates in the selected East and North columns. If a non-earth projection is selected the data can still be opened in ArcGIS but not overlain with other projected datasets.
2. Display an Attribute Map as the active window and set the colour, shape, size and visibility as desired.
3. Select Map>Export to ArcGIS or click on the icon on the Attribute Map RHS (Right-Hand Side) Toolbar.
4. Assign a name and location for the Geodatabase and layer file and click Export.
5. Open ArcGIS and click on Add Data. Browse to the geodatabase and open.
Export to MapInfo
This option will save an Attribute Map or Ranked Variable Map including any colour, shape, size and visibility attributes and export them to a MapInfo TAB file. The associated legend window will be exported as a separate MapInfo TAB file as well.
Page 47 of 48
The Export to MapInfo utility can only be run using the ioGAS 32-bit version.
1. In the Column Properties dialog make sure that the East/North Projection is selected to match the coordinates in the selected East and North columns. If a non-earth projection is selected the data can still be opened in MapInfo but not overlain with other projected datasets.
2. Display an Attribute Map or Ranked Variable Map as the active window and set the colour, shape, size and visibility as desired.
3. Select Map>Export to MapInfo or click on the icon on the Attribute Map or Ranked Variable Map RHS (Right-Hand Side) Toolbar.
4. Assign a name and location for the MapInfo file and click Export.
5. Open MapInfo and select File>Open. Browse to the TAB file and open.
ioGAS Link for GOCAD
The ioGAS Link for GOCAD is a live link that enables data to be worked with in real time in either ioGAS or GOCAD and for the changes to be viewed in both programs. This utility must be purchased separately.
See GOCAD Live Link for more information on how this works.
ioGAS Link for Leapfrog Geo
The ioGAS Link for Leapfrog Geo is a live link that enables data to be worked with in real time in either ioGAS or Leapfrog Geo and for the changes to be viewed in both programs. This utility must be purchased separately.
See Leapfrog Geo Live Link for more information on how this works.
For additional Help see the relevant sections in this Help file. Maintained users can also access a series of training videos via the Help>Training Videos menu option.
Page 48 of 48
Getting Help
Help System
For detailed descriptions on how to use each feature within ioGAS select the relevant topic from the Table of Contents in the Help file (Help>Help menu option) and browse the various topics using the links.
Training Videos
Maintained users are able to view our full range of training videos which outline how to use the various features within ioGAS. To access the videos select the Help>Training Videos (web) menu option. This menu item will not be available to non-maintained users. To purchase maintenance please contact [email protected]
Frequently Asked Questions
Browse the FAQ section on our website for answers to commonly asked ioGAS questions.
Technical Support
Email support is available for maintained clients. New clients are automatically entitled to 12 months support and upgrades from their date of purchase but ongoing maintenance must be purchased after this time in order to be eligible for technical support and software upgrades.
It is also possible to log any issues or enhancement requests using this technical support email address and we always welcome client feedback to help us to continually improve our software.
Contact Details:
Email: [email protected]
Where possible try to include a screen capture of the Help>About dialog and a copy of any log.txt files located in the C:\Users\Username\AppData\Roaming\ioGAS\log folder (PC Users) or the Applications\ioGAS\Contents\Resources\app\data folder (MAC Users). (Username = your login)
Note that E-mail support is not intended for providing remote training. If you would like to enquire about available training please contact [email protected]
