Outlineday4–May30th

•  GraphinginR:– basicgraphing– ggplot2package

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GraphinginR:basicgraphing

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Producinggraphs

•  R-basepackagegraphicsoffersfuncAonsforproducingmanyplots,forexample:–  scaFerplots–plot()–  histograma–hist()–  boxplots–boxplot()–  barplots–barplot()–  piecharts–pie()

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basicgraphing

ScaFerplots

Asca&erplotisatypeofplotormathema2caldiagramusingCartesiancoordinatestodisplayvaluesfortypicallytwovariablesforasetofdata.[Wikipedia]

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basicgraphing

BasicscaFerplot

•  x<-1:10•  y<-x^2•  plot(x,y)

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basicgraphing

ScaFerplot

•  plot(x,y,col="red",pch=2,type="b",main="apre?ysca?erplot")

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basicgraphing

ScaFerplot

•  plot(x,y,col=1:10,pch=1:10,cex=1:10,type="b",main="apre?ysca?erplot")

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basicgraphing

Barplots

Abarchartorbargraphisachartthatpresentsgroupeddatawithrectangularbarswithlengthspropor2onaltothevaluesthattheyrepresent.[Wikipedia]

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basicgraphing

Barplot•  x<-rep(c("geek","nerd","dork"),c(10,5,3))

•  barplot(table(x))

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basicgraphing

Piechart

Apiechartisacircularsta2s2calgraphicwhichisdividedintoslicestoillustratenumericalpropor2on.[Wikipedia]

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basicgraphing

Piechart•  x<-rep(c("geek","nerd","dork"),c(10,5,3))

•  pie(table(x))

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basicgraphing

Boxplots

Indescrip2vesta2s2cs,aboxplotisaconvenientwayofgraphicallydepic2nggroupsofnumericaldatathroughtheirquar2les.

[Wikipedia]

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basicgraphing

Boxplots•  x<-matrix(rnorm(1000),ncol=2)

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basicgraphing

Histograms

Ahistogramisaplotthatletsyoudiscover,andshow,theunderlyingfrequencydistribu2onofasetofcon2nuousdata.

[Wikipedia]

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basicgraphing

Histogram•  x<-rnorm(200)•  hist(x)

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basicgraphing

ExporAnggraphs

•  Graphscanbesavedintomanyformats,including:pdf,jpeg,bmp,Dff.

•  Openthefiletosaveyourplotin: pdf("my_graph.pdf")

•  Produceagraph: plot(1:10)

•  Andcloseit: dev.off()

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basicgraphing

ExporAnggraphs•  FromRStudio:

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basicgraphing

Exercise9:Basicplots

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GraphinginR:IntroducDontoggplot2package

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ggplot2

•  GraphingpackageinspiredbytheGrammarofGraphicsseminalworkofLelandWilkinson.

•  Atoolthatenablestoconciselydescribethecomponentsofagraphic.

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graphinginR:ggplot2

ggplot2

•  Flexible•  Customizable•  PreFy•  Welldocumented

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graphinginR:ggplot2

ggplot2

•  Baselayertoplottwovariables:

ggplot(dataframe,aes(x,y))

•  Addlayerspecifyingwhatkindofplotyouwant.ExampleofascaFerplot:

ggplot(dataframe,aes(x,y))+geom_point()

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graphinginR:ggplot2

ScaFerplots

•  df1<-data.frame(sample1=rnorm(200),sample2=rnorm(200))

•  ggplot(df1,aes(x=sample1,y=sample2))+geom_point()

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graphinginR:ggplot2

ScaFerplots

•  Storethegraphinanobject:p<-ggplot(df1,aes(x=sample1,y=sample2))+geom_point()

•  addlayerstop:–  AtlewithggDtle("myAtle")–  verAcallinewithgeom_vline(xintercept=2)–  etc.

•  p+ggAtle(…)

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ScaFerplots

p<-ggplot(df1,aes(x=sample1,y=sample2))+geom_point()•  addAtlewithggDtle

p2<-p+ggDtle("Atleoftheplot")

•  drawaverAcalwithgeom_vlinep3<-p2+geom_vline(xintercept=0)

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graphinginR:ggplot2

ScaFerplots

•  Coloraccordingtoanothercolumn:

df2<-data.frame(df1,grouping=rep(c("yes","no"),c(80,120)))p<-ggplot(df2,aes(sample1,sample2,color=grouping))+geom_point()

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graphinginR:ggplot2

ScaFerplots

•  p<-ggplot(df2,aes(sample1,sample2,color=grouping))+geom_point()

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graphinginR:ggplot2

Boxplots

•  ggplot(df2,aes(x=1,y=sample1))+geom_boxplot()

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graphinginR:ggplot2

Boxplotsggplot(df2,aes(x=grouping,y=sample1))+geom_boxplot()

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graphinginR:ggplot2

Boxplots

Plofngbothsample1andsample2?Needtoconvertthedataframeintoalongformat!

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graphinginR:ggplot2

Widevslongformats

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graphinginR:ggplot2

genename sample1 sample2 grouping

gene1 6 3 UP

gene2 2.7 5.1 DOWN

gene3 3.2 3.3 NONE

gene4 4.7 1.1 UP genename grouping variable value

gene1 UP sample1 6

gene2 DOWN sample1 2.7

gene3 NONE sample1 3.2

gene4 UP sample1 4.7

gene1 UP sample2 3

gene2 DOWN sample2 5.1

gene3 NONE sample2 3.3

gene4 UP sample2 1.1

library(reshape2)?melt

wide

long

Boxplots

Plofngbothsample1andsample2?Converttolongformatdf_long<-melt(df2)

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graphinginR:ggplot2

Boxplots

ggplot(df_long,aes(x=variable,y=value))+geom_boxplot()

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graphinginR:ggplot2

Boxplots

ggplot(df_long,aes(x=variable,y=value,color=grouping))+geom_boxplot()

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graphinginR:ggplot2

Barplots

•  p<-ggplot(df2,aes(x=grouping))+geom_bar()

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Barplots

•  p<-ggplot(df2,aes(x=grouping))+geom_bar()

•  Changexaxislabelwithscale_x_discrete:p2<-p+scale_x_discrete(name=”Howmanyyesandno")

•  Swappingxandyaxiswithcoord_flip():p3<-p2+coord_flip()

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graphinginR:ggplot2

Barplots

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graphinginR:ggplot2

Histograms

•  ggplot(df_long,aes(x=value))+geom_histogram()

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graphinginR:ggplot2

Histograms

•  ggplot(df_long,aes(x=value,fill=variable))+geom_histogram()

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graphinginR:ggplot2

default:stacked!

Histograms

•  ggplot(df_long,aes(x=value,fill=variable))+geom_histogram(posiAon='idenAty')

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graphinginR:ggplot2

Histograms

•  ggplot(df_long,aes(x=value,fill=variable))+geom_histogram(posiAon='dodge')

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graphinginR:ggplot2

Exercise10:IntroducDontoggplot2

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Wrapup:whatdidwelearninthose12hours?

•  RStudio•  Datastructures– Vector– Matrix– Dataframe– Lists

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•  Input/Output•  Packages•  Plofng– basicplofng– ggplot2

What’snext?

•  Statsnextweek!

•  Loops•  FuncAons•  RMarkDown...Anythingyouwanttolearn?à Contactsarah.bonnin@crg.euand/ordamjana.kastelic@crg.eu

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RStudioCheatsheets

hFps://www.rstudio.com/resources/cheatsheets/hFps://www.rstudio.com/wp-content/uploads/2016/11/ggplot2-cheatsheet-2.1.pdf

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Onlinecourses

EDX/Courseracourses:hFps://www.coursera.org/learn/r-programminghFps://www.coursera.org/learn/advanced-rhFps://www.coursera.org/specializaAons/staAsAcshFps://www.edx.org/course/introducAon-r-data-science-microsos-dat204x-4hFps://www.edx.org/course/staAsAcs-r-harvardx-ph525-1x-0

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Forums

Rmailinglists:hFps://www.r-project.org/mail.htmlBioconductorforum:hFps://support.bioconductor.org/

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SarahBonnin–sarah.bonnin@crg.euCRGBioinformaAcsunitEstefaniaMancini–estefania.mancini@crg.euLabJuanValcárcel

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Thanks!

Moreusefulbasiccommands

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SomecommonarithmeAcfuncAons

naturallogarithm log(x)exponenAalfuncAon

e^x exp(x)

sine sin(x)

cosine cos(x)

tangent tan(x)

absolutevalue abs(x)

squareroot sqrt(x)

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Morecommands

Objectsstoredintheglobalenvironment

•  LisAng:ls()orobjects()•  Removingoneobjectfromenvironment:rm(x)•  Removingseveralobjects:rm(x,y)

•  Removingallobjectfromenvironment:rm(list=ls())

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Morecommands

Savingobjectsorsession

•  Saveobjectsxandyinto"myobjects.RData"file– save(x,y,file="myobjects.RData")

•  Loadobjectsxandyintocurrentdirectory:–  load("myobjects.RData")

•  Savethecurrentworkspace(allobjects):– save.image(file=".RData")

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Morecommands

Commandhistory

•  Last25commands:–  history()

•  Allpreviouscommands–  history(max.show=Inf)

•  Savecommandhistory:–  savehistory()

•  Loadcommandhistory:–  loadhistory()

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Morecommands

InformaAonaboutthecurrentsession

sessionInfo()

Rversion

Pla\ormandOSversion

Packagesa?ached

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Morecommands

WriDngfuncDonsinR

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User-wriFenfuncAons

•  FuncAonsarepiecesofcodewriFentocarryoutspecifiedtasksandbeabletorepeatthemeasily.

•  RallowsyoutocreateyourownfuncAons.

Func=ons

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FuncAons’structure

myfuncDon<-funcDon(arg1,arg2,...){ commands return(something)}

Func=ons

FuncDon’sname CreaDngthefuncDon

myfuncDon’slistofarguments

whatmyfuncDondoes

Value/objectmyfuncDonreturns

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ObjectsinfuncAonsmyfuncDon<-funcDon(arg1){a<-arg1return(a+1)

}

Func=ons

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>a<-12>myfuncAon(10)[1]11>a[1]12

>myfuncAon(10)[1]11>aError:object'a'notfound