How can I extract the matrix derived from a heatmap created with gplots after hierarchical clustering?

Question

I am making a heatmap, but I can't assign the result in a variable to check the result before plotting. Rstudio plot it automatically. I would like to get the list of rownames in the order of the heatmap. I'am not sure if this is possible. I'am using this code:

hm <-    heatmap.2( assay(vsd)[ topVarGenes, ], scale="row", 
         trace="none", dendrogram="both", 
         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255),
         ColSideColors = c(Controle="gray", Col1.7G2="darkgreen", JG="blue", Mix="orange")[
           colData(vsd)$condition ] )

Answer 1

You can assign the plot to an object. The plot will still be drawn in the plot window, however, you'll also get a list with all the data for each plot element. Then you just need to extract the desired plot elements from the list. For example:

library(gplots)

p = heatmap.2(as.matrix(mtcars), dendrogram="both", scale="row")

p is a list with all the elements of the plot.

p # Outputs all the data in the list; lots of output to the console

str(p) # Struture of p; also lots of output to the console

names(p) # Names of all the list elements

p$rowInd # Ordering of the data rows

p$carpet # The heatmap values

You'll see all the other values associated with the dendrogram and the heatmap if you explore the list elements.

Answer 2

To others out there, a more complete description way to capture a matrix representation of the heatmap created by gplots:

matrix_map <- p$carpet
matrix_map <- t(matrix_map)