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## Julia Bischof
## 10-09-2015
#library(gplots)
plotGeneComb<-function(geneComb.tab=NULL,color=c("gray97","darkblue"), withNA=TRUE,title=NULL, PDF=NULL,...){
if(length(geneComb.tab)==0){
stop('--> Gene combination table is missing')
}
if(length(color)==1){
color<-c("white",color)
}
if(max(geneComb.tab,na.rm=T)>1){
geneComb.tab<-geneComb.tab/sum(geneComb.tab,na.rm=T)
}
if(nrow(geneComb.tab)<ncol(geneComb.tab)){
geneComb.tab<-(t(geneComb.tab))
}
if(length(PDF)>0){
pdf(file = paste(PDF,"_",substr(colnames(geneComb.tab)[1],1,4),"-",substr(rownames(geneComb.tab)[1],1,4),"-combinations.pdf",sep=""),
width = nrow(geneComb.tab)+8,
height = ncol(geneComb.tab)+3,
pointsize = if(sqrt(min(dim(geneComb.tab))*min(dim(geneComb.tab)))<18){18}else{round(sqrt(min(dim(geneComb.tab))*min(dim(geneComb.tab)))+10,-1)})
}
if(withNA==FALSE){
geneComb.tab<-geneComb.tab[-which(rownames(geneComb.tab)=="NA"),-which(colnames(geneComb.tab)=="NA")]
}
par(oma=c(nchar(colnames(geneComb.tab)[1])*0.6,1,2,nchar(colnames(geneComb.tab)[1])*0.6))
heatmap.2(t(as.matrix(geneComb.tab)),col=colorRampPalette(c(color[1],color[2])),Rowv=T,Colv=T,key=T,density.info="none",
main=if(length(title)==0){paste(substr(colnames(geneComb.tab)[1],1,4), " & ", substr(rownames(geneComb.tab)[1],1,4)," combinations",sep="")}else{title},
trace="none",cexCol=1.3,cexRow=1.3,dendrogram="none",key.xlab="proportion",key.par=list(cex=0.9),cex.main=1.4)
if(length(PDF)>0){
dev.off()
}
}
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