heatmap in R how to resize columns labels?

Question

I have a data.matrix that is approximately 4000 rows and 100 columns. I am doing a heatmap of the data like:

data<-heatmap(data_matrix,Rowv=NA,Colv=NA,col=cm.colors(256),scale="column",margins=c(5,10))

But the problem that I got is that the labels that appear in the column are too grouped, so it is impossible to visualize them correctly. How I can resize the heatmap so I can see the values of the labels of the column? I tried to print it in pdf, but it only appears a black stripe. Thanks

I am including a figure of the heatmap, the portion that I want to see are the labels that are in the right part, but they are too close together.

Answer 1

First of all it's better to put your output directly to a PDF file - you may use other image formats but PDF is the best because it is a vector output and you can zoom as much as you want:

pdf("Your-file.pdf", paper="a4", width=8, height=8)

Then it's better to use pheatmap ( = pretty heatmap) package. It makes really better heatmaps with a color key besides your heatmap. Finally although the pheatmap() function tries to reduce the label size while you have many rows, but it fails for really large number of rows. So I use the code below for really high - but not too high - number of rows:

library(pheatmap)   
library(gplots)
if (nrow(table) > 100) stop("Too many rows for heatmap, who can read?!")
fontsize_row = 10 - nrow(table) / 15
pheatmap(table, col=greenred(256), main="My Heatmap", cluster_cols=F, 
         fontsize_row=fontsize_row, border_color=NA)

You may change fontsize_col for the column labels. You have many interesting options like display_numbers to have the values inside the cells of your heatmap. Just read ?pheatmap .

This is an example generated by the default parameters of pheatmap() command:

Finally note that too many rows are easy to read on a display, but useless for print.

Answer 2

In Rstudio you can easily resize the graphic window, same holds for Rgui. Alternatively, if you save the plot to file you can use a bigger size for your graphics, eg bigger width and height when calling pdf or png .

Answer 3

You can use cexRow = and cexCol =.

You can get more information into ??heatmap.2

# Row/Column Labeling
margins = c(5, 5),
ColSideColors,
RowSideColors,
cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
srtRow = NULL,
srtCol = NULL,
adjRow = c(0,NA),
adjCol = c(NA,0),
offsetRow = 0.5,
offsetCol = 0.5,
colRow = NULL,
colCol = NULL

Answer 4

If you use pheatmap ( https://www.rdocumentation.org/packages/COMPASS/versions/1.10.2/topics/pheatmap ) you can spread out those labels by adjusting the cellheight parameter.

If you are doing this in R notebook, even though the entire heat map will not display in your output window when you run the code, when you save the heat map to your computer using the filename parameter, pheatmap will automatically calculate the optimal size for the output file so that your entire heatmap will be displayed in your output file. If this size is not to your liking you can adjust using width and height parameters, but it is unlikely you will want to do this.