Heatmap2 missing some genes

Question

[ovariohisterectomia]

Hi everyone, this is maybe a very short question.

I have a table like this (each letter is a gene)

A
B
C
D
E
F
G
H
I
J
K

After that, I want to generate a Heatmap, with this script

head(highly_variable_lcpm)
heatmap.2(as.matrix(highly_variable_lcpm),
          col=color1,
          trace="none", 
          main="Top 100 de genes con mayor variabilidad",
          #ColSideColors=col.cell,
          density.info="none",
          Colv="NA",
      Rowv=FALSE, 
          scale="row")

This script shows me a nice Heatmap, but the problem is that only shows me B, D, F, H, J genes.

The question is, is there any parameter that I can add or modify to tell the script that shows me all genes? I tried to generate the table with less genes, but is the same. If I generate a table with 100 genes, the heatmap shows me 50 genes (one yes, one no, one yes, one no, etc) , if I generate a table with 50 genes it shows me 25...and then...

Would you please help me? thank you in advance!

[Asaf]

So it only shows half of the labels?

Answer 1

[Jean-Karim Heriche]

It looks like every other label is not displayed. This is usually because there's not enough space to display all of them. One option is to reduce the font size of the labels using parameters like cexRow and cexCol, another option is to make the image bigger using the lmat, lwid and lhei parameters. Check the docs.

You may find this previous post listing various tutorials on heatmaps in R useful.

[ovariohisterectomia]

thank you! it was the problem, cexRox and cexCol were the solution, there was not enough space to display all genes thank you!

[Ram]

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