//Example plotting in R //A.M. Larracuente for Bio472 Section 3 //Example scripts, data and plots are found in /scratch/bio472_2014/Example_scripts/R_examples/ //Read in example dataset of various covariates for Drosophila melanogaster //Data from: Larracuente, A.M., T.B. Sackton, A.J. Greenberg, A. Wong, N.D. Singh, D. Sturgill, Y. Zhang, B. Oliver, A.G. Clark. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24(3): 114-123. cov=read.table("/scratch/bio472_2014/Example_scripts/R_examples/Larracuente_covariate_table.txt",header=T) //eg 1 //Make a boxplot of Expression level (average whole body expression in FlyAtlas) by cellular location boxplot(FlyAtlasWhole.New~CellularLocation,data=cov,notch=T,ylab="Expression rank")

//eg2 //Make a density plot of dS and dN plot(density(cov$dN),xlim=c(0,3),xlab="substitutions per site",main="dN and dS") lines(density(cov$dS),col="red",lty=2) legend("topright",inset=c(.01,.01),c("dN","dS"),col=c("black","red"),lty=c(1,2))

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//eg3 //Make a scatterplot of recombination rate and omega (dN/dS), fit a line and plot it plot(cov$Recomb.ACE,cov$w, xlab="Recombination rate",ylab="omega",pch=20) cor.test(cov$w,cov$Recomb.ACE) z=lm(w~Recomb.ACE,data=cov) abline(z,col="grey")

//eg4 //Make a histogram of intron number counts hist(cov$Intron.Num,col="light blue",xlab="Number of introns",ylab="Count",main="")

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//eg5 //Plot RPM according to genomic location with the sign corresponding to the strand (negative RPM for - strand and positive RPM for + strand) //First read in RPM file called test_piRNA_RPM.txt and then load (first install if you don't have) ggplot2 //code modified from J. Vedanayagam //Also see useful plots here:http://www.ark-genomics.org/bioinformatics/virome pirna=read.table("/scratch/bio472_2014/Example_scripts/R_examples/test_piRNA_RPM.txt") library(ggplot2) ggplot(pirna, aes(x=pirna$V1, y=pirna$V2, fill=pirna$V3))+ geom_bar(stat="identity", position="identity")+ scale_y_continuous(limits=c(-15,15))+ scale_fill_manual(values=c("orange","blue"), guide=FALSE)+ xlab("Position (bp)")+ ylab("RPM")+ theme(panel.background = element_rect(colour = "black", fill = "white"))+ theme(panel.grid.major = element_blank())+ theme(panel.grid.minor = element_blank())+ geom_hline(yintercept=0, size=0.15,colour="light grey")+ theme(axis.text = element_text(colour = "black"))+ theme(axis.ticks = element_line(colour = "black"))

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//eg6 //Make boxplots for multiple variables using par(new=T). In this example, we'll grab subsets of the dataframe to plot separately TEcount=read.table("~/scratch/bio472_2014/Example_scripts/R_examples/TE.countsforR.txt",header=T) shar=TEcount[TEcount$Status=="Shared",] non=TEcount[TEcount$Status=="Non-reference",] ref=TEcount[TEcount$Status=="Reference",] boxplot(Count~TE,data=shar,boxwex=.2,col="red",at=c(1:67)-.5,axes=F,border="pink",outwex=.01) boxplot(Count~TE,data=non,boxwex=.2,col="green",at=c(1:67)-.1,add=T,axes=F,border="dark olivegreen2",outwex=.01) boxplot(Count~TE,data=ref,boxwex=.2,col="blue",at=c(1:67)-.3,add=T,ylab="Counts",border="light blue",outwex=.01,las=2)

legend("topright",inset=c(.01,.01),c("Ref","NonRef","Shared"),fill=c("red","blue","green"))

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//eg7 //Make stacked barplots. In this example, we'll flip the table so the rows become columns and vice versa (this is done with t() ). TEbar=read.table("~/scratch/bio472_2014/Example_scripts/R_examples/TE.countsforRbarplot.txt",header=T) TEcol=cbind(TEbar$X2L_shared,TEbar$X2L_Ref,TEbar$X2L_Nonref,TEbar$X2R_shared,TEbar$X2R_Ref,TEbar$X2R_Nonref) barplot(t(as.matrix(TEcol)),names=TEbar[,1],col=c("red","blue","green","orange","light blue","purple"),las=2,cex.names=.8,legend=c("2L_shared","2L_Ref","2L_Nonref","2R_shared","2R_Ref","2R_Nonref"))

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