Make row labels italic in heatmap.2

Question

I'm trying to make my row labels italic using the R function heatmap.2. There's no default option and I can't figure out a work around by setting par(font=3) for example. How can I set my row labels to be italic in heatmap.2?

set.seed(123)
data = matrix(sample(100), nrow=10, ncol=10)
rownames(data) = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J")

library(gplots)

heatmap.2(data,
           Colv=TRUE,
           Rowv=TRUE,
           xlab=NA,
           ylab=NA)

`expression(italic())` works here. Just need to figure out a way to sneak it into `heatmap.2` function. — M--, Jul 25 '19 at 18:44
Unfortunately, that only results in a row labeled: italic("B"). Any suggestions on how to approach sneaking it into heatmap.2? — Erik, Jul 25 '19 at 23:08
Run `heatmap2` without any arguments. The source code will apear. You need to change the `axis(...)` function. — M--, Jul 25 '19 at 23:12

score 4 · Accepted Answer · answered Jul 26 '19 at 16:37

You can use the labCol and labRow arguments to heatmap.2 to pass in the labels. We just need to figure out how to pass these in as a list of plotmath expressions. I always find this painful, as I don't do it often enough to remember the appropriate incantations, but was able to put the code together by adapting this R-help answer. Note that the matrix needs to have column names, which I've added in the code below

library(gplots)

# Fake data
set.seed(123)
data = matrix(sample(100), nrow=10, ncol=10)
rownames(data) = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J")
colnames(data) = 1:ncol(data)

heatmap.2(data,
          Colv=TRUE,
          Rowv=TRUE,
          labCol=as.expression(lapply(colnames(data), function(a) bquote(italic(.(a))))),
          labRow=as.expression(lapply(rownames(data), function(a) bquote(italic(.(a))))),
          xlab=NA,
          ylab=NA)

Make row labels italic in heatmap.2

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