How to force the row labels in a fixed width and be aligned in pheatmap in R?

Question

Usually there is no problem to show the row labels in pheatmap in R. However, see I have a little bit complicated row labels which are strings that combined a head of one string and an end of another string. For example, "ABC**** 123".

Here is an example and my code:

library(pheatmap)
library(stringr)

# create an example
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

# make random pvalue to show at the end of rownames
random.pvalue <- formatC(runif(n = 20,min = 0.0000000000001,max = 0.00000000001),format = "e",
                         digits = 2)

# creat new rownames with fixed width
add.label <- paste0(str_pad(rownames(test),
                    width=12, 
                    side="right"),
                    random.pvalue)

rownames(test) <- add.label # update rownames
# Draw heatmaps
pheatmap(test) # you could see the pvalues are not aligned

Trust me I have forced these row labels in a fixed width by using formatC() and str_pad() in R. However, when I used pheatmap with those row labels, the labels did not show as I thought, they went like the following, and you can clearly see that the row labels are not aligned even they have the same string width.

 [1] "Gene1       7.77e-12" "Gene2       2.67e-12" "Gene3       8.67e-12" "Gene4       6.61e-12"
 [5] "Gene5       2.36e-12" "Gene6       3.09e-12" "Gene7       5.44e-12" "Gene8       3.18e-13"
 [9] "Gene9       1.34e-12" "Gene10      4.52e-12" "Gene11      2.03e-12" "Gene12      5.31e-12"
[13] "Gene13      9.66e-12" "Gene14      9.02e-12" "Gene15      2.91e-13" "Gene16      7.37e-13"
[17] "Gene17      7.95e-12" "Gene18      8.04e-12" "Gene19      8.31e-12" "Gene20      9.94e-12"

Maybe someone could use a simple example to teach me how to fix this.

Many thanks advanced!

Hi Sugus. Please add a [minimale reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example/5963610#5963610). The definition of minimal rep. example is exactly **not** to upload your data, but to give only so much (and not more) data and code as is needed to reproduce your problem. That way you can help others to help you! — dario, Feb 22 '20 at 15:38

score 1 · Accepted Answer · answered Feb 23 '20 at 02:09

You could use a fixed font (not a proportional one):

library(pheatmap)
library(grid)
library(stringr)
mat <- mtcars[1:10,1:6]
rn <- stringr::str_pad(rownames(mat), max(nchar(rownames(mat))), side = "right")
p <- signif(1e-9*mat[,4], digits = 4)
pheatmap::pheatmap(as.matrix(mtcars[1:10,1:6]), scale="column", 
    labels_row=paste(rn, p, sep="    "), fontfamily = "mono")

How to force the row labels in a fixed width and be aligned in pheatmap in R?

1 Answers1