CODEWITHSUNDEEP
rheatmap
Krzysztof Polanski
Krzysztof Polanski

Reputation: 125

R heatmap - how to get uniform colour map?

I'm trying to get a heatmap to work in R, but I've noticed some rather erratic behaviour of the colour maps. Small extract from the data:

data = matrix(c(0,0,1,1,1,2,2,2,2,2,1,1,1,0,1,1,1,1,1,1,0,0,0,0,0),5,5,byrow=TRUE)

This yields a 5x5 matrix, with three of the rows being occupied by all 2's, all 1's and all 0's respectively. However, when I try to apply a colour map, I get pure white on all three of those rows, instead of different colours as expected.

library(RColorBrewer)
heatmap(data,col=brewer.pal(3,'RdBu'),Colv=NA,Rowv=NA)

The resulting heatmap

It's not the colour map of choice being wonky, I observe analogous behaviour when I leave the default colour map on. What's going on here, how do I make this go away? I want the 0's to be one colour, the 1's to be one colour, the 2's to be one colour. In the grand scope of things, I also need to be able to add separately computed dendrograms to the rows/columns, with the dendrograms not being convertible to hclusts because of reasons beyond my control, what makes pheatmap not an immediately viable solution.

Upvotes: 0

Views: 124

Answers (1)

Krzysztof Polanski
Krzysztof Polanski

Reputation: 125

Immediately after submitting this question, I found the scale option of the heatmap. The solution thus becomes:

heatmap(data,col=brewer.pal(3,'RdBu'),Colv=NA,Rowv=NA,scale="none")

As intended

Apologies, I'll show myself out

Upvotes: 1

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