Sorted hetamap using R

Question

[####]

I want to generate the sorted heatmaps based on the expression, what function I have to use to get the sorted heatmap based on expression, here is the script I wrote to generate the heatmap:

  library(gplots) a <- read.csv("heatmap_input.csv",sep=",")
  row.names(a) <- a$Gene 
  a  <- a[,2:6]
  a_matrix <- data.matrix(a)
  cR=c(0.85) 
  cols= colorpanel(20,'blue','black','yellow')
  a_heatmap <-  heatmap.2(a_matrix,col=cols,dendrogram='row',Colv=NA,key=TRUE,keysize = 
  1.0, main = 'ctrl vs treated', density.info="none",trace="none",cexRow=cR,scale="row",   margins=c(5,5))

[Maxime Lamontagne]

I think you need to order the data yourself before making the heatmap. Also, sorted based on expression is unclear.

[Jean-Karim Heriche]

Look at the parameters Rowv and Colv of heatmap.2().

[####]

Colv shall help me , but its ordering all the columns , but lets say I want sample group wise lets say unregulated on the top or down regulated at the bottom or viceversa

[Jean-Karim Heriche]

I think you can give a vector of indices to Colv so you generate the ordering you want and pass this as Colv argument. Alternatively, reorder your data matrix and use Colv = FALSE.