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#Within R #Install and Load libraries install.packages("gplots") install.packages("pheatmap") library("DESeq2") library("RColorBrewer") library("gplots") library( "genefilter" ) library("pheatmap") #I've already run DESEQ2 on this experiment for you. Just load the results load("deseq2.kallisto.RData") #Regularized log transformation rld <- rlog( dds ) #Get 25 top varying genes topVarGenes <- head( order( rowVars( assay(rld) ), decreasing=TRUE ), 25) #Use heatmap.2 function to draw a heatmap #INCLUDE NEXT LINE IF YOU WANT TO SAVE THE FIGURE IN A FILE #png#pdf(file="gene.heatmap.pngpdf",width=500,height=500,res=72) heatmap.2( assay(rld)[ topVarGenes, ], scale="row",trace="none", dendrogram="column",col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) #INCLUDE NEXT LINE IF YOU WANT TO SAVE THE FIGURE IN A FILE #dev.off() #PLOT PCA #INCLUDE NEXT LINE IF YOU WANT TO SAVE THE FIGURE IN A FILE #png#pdf(file="pca.pngpdf",width=400,height=350,res=72) print(plotPCA(rld, intgroup=c("condition"))) #INCLUDE NEXT LINE IF YOU WANT TO SAVE THE FIGURE IN A FILE #dev.off() |
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