An Improved Heatmap Package

An improved heatmap package. Completely compatible with the original R function heatmap, and provides more powerful and convenient features.

heatmap3

• Introduction
• Download and install
• Example
• Reproduce the figures

install.packages("heatmap3")

#Load heatmap3 package
library(heatmap3)
#View help files
?heatmap3
#The examples of heatmap3 and other functions
example(heatmap3)
example(showLegend)
example(showAnn)
example(colByValue)

First you will need to download the count data. We generate the count data based on the TCGA BRCA samples. You can use the following codes in Linux system to download the count data. Or you can download it in github release page.

wget https://github.com/slzhao/heatmap3/releases/download/example/allSample_edgeR_result.csv
wget https://github.com/slzhao/heatmap3/releases/download/example/BRCA_30Samples.csv
wget https://github.com/slzhao/heatmap3/releases/download/example/BRCA_30Samples_clinic.csv

Here are the R codes to generate the figures.

#Assume you have already installed heatmap3 package. And the 3 example file were download in current working directory. You can use the following codes in R to generate the figures.

#Prepare expression data
counts<-read.csv("BRCA_30Samples.csv",header=T,row.names=1)
#Prepare column side annotation
clinic<-read.csv("BRCA_30Samples_clinic.csv",header=T,row.names=1)
#Prepare row side color bar annotation
edgeR_result<-read.csv("allSample_edgeR_result.csv",header=T,row.names=1)
temp1<-(edgeR_result$logFC)
temp2<--log10(edgeR_result$FDR)
temp1<-colByValue(as.matrix(temp1),range=c(-4,4),col=colorRampPalette(c('chartreuse4','white','firebrick'))(1024))
temp2<-colByValue(as.matrix(temp2),range=c(0,5),col=heat.colors(1024))
colGene<-cbind(temp1,temp2)
row.names(colGene)<-row.names(edgeR_result)
colnames(colGene)<-c("log2FC","-Log10P")

#Generate Figure1
#counts, colGene and clinic were read throught the csv file
##Assume counts has counts information for each gene, colGene has the colors for each gene, clinic has the clinic information for each sample
temp<-apply(counts,1,sd)
selectedGenes<-rev(order(temp))[1:500]
heatmap3(counts[selectedGenes,],labRow="",margin=c(7,0),RowSideColors=colGene[selectedGenes,],ColSideCut=0.85,ColSideAnn=clinic,ColSideFun=function(x) showAnn(x),ColSideWidth=1.2,balanceColor=T)

#Generate Figure2
heatmap3(counts,topN=c(500,3000,nrow(counts)),Rowv=NA,labRow="",margin=c(7,0),RowSideColors=colGene,ColSideCut=0.85,ColSideAnn=clinic,ColSideFun=function(x) showAnn(x),ColSideWidth=1.2,balanceColor=T)

Here is the environment (including the version of packages).

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] heatmap3_1.0.3

loaded via a namespace (and not attached):
[1] fastcluster_1.1.13 tools_3.0.2