# NOT RUN {
#gererate data
set.seed(123456789)
rnormData<-matrix(rnorm(1000), 40, 25)
rnormData[1:15, seq(6, 25, 2)] = rnormData[1:15, seq(6, 25, 2)] + 2
rnormData[16:40, seq(7, 25, 2)] = rnormData[16:40, seq(7, 25, 2)] + 4
colnames(rnormData)<-c(paste("Control", 1:5, sep = ""),
paste(c("TrtA", "TrtB"), rep(1:10,each=2), sep = ""))
rownames(rnormData)<-paste("Probe", 1:40, sep = "")
ColSideColors<-cbind(Group1=c(rep("steelblue2",5), rep(c("brown1",
"mediumpurple2"),10)),Group2=sample(c("steelblue2","brown1",
"mediumpurple2"),25,replace=TRUE))
colorCell<-data.frame(row=c(1,3,5),col=c(2,4,6),color=c("green4",
"black","orange2"),stringsAsFactors=FALSE)
highlightCell<-data.frame(row=c(2,4,6),col=c(1,3,5),color=c("black",
"green4","orange2"),lwd=1:3,stringsAsFactors=FALSE)
#A simple example
heatmap3(rnormData,ColSideColors=ColSideColors,showRowDendro=FALSE,
colorCell=colorCell,highlightCell=highlightCell)
#A more detail example
ColSideAnn<-data.frame(Information=rnorm(25),Group=c(rep("Control",5),
rep(c("TrtA","TrtB"),10)),stringsAsFactors=TRUE)
row.names(ColSideAnn)<-colnames(rnormData)
RowSideColors<-colorRampPalette(c("chartreuse4", "white",
"firebrick"))(40)
result<-heatmap3(rnormData,ColSideCut=1.2,ColSideAnn=ColSideAnn,
ColSideFun=function(x) showAnn(x),ColSideWidth=0.8,
RowSideColors=RowSideColors,col=colorRampPalette(c("green","black"
, "red"))(1024),RowAxisColors=1,legendfun=function()
showLegend(legend=c("Low","High"),col=c("chartreuse4","firebrick"))
,verbose=TRUE)
#annotations distribution in different clusters and the result
#of statistic tests
result$cutTable
# }
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