Display only a subset of rownames in heatmap?

Question

[johnlee.johnson]

Hi everyone,

I am trying to create a heatmap in R that has about 20,000 rows and I want to display the rownames, which it does by default. The problem is that there are too many rows to display the names correctly, and only about 50 of the rownames have any real meaning. Is there any package or method in R to subset the rownames and have it display only the ones I want? I have tried setting a blank in the rownames I don't want, and keep only the rownames I want, but the labels only show up when I limit the heatmap to about 500 rows or so, and trying to increase the font size does not help.

I would like to keep all 20,000 rows because it shows the genome wide regulation pattern that I'm trying to portray in the figure, but for a subset of genes I'd like to display their approximate position in the heatmap to give a sense of where they fit in the overall pattern.

Thanks!

Answer 1

[Sean Davis]

Using heatmap.2, for example, you can pass in a vector of row names as labRow, a character vector. Just make the row names for the "uninteresting rows" blank ("").