How do I put the color scales on heatmap.2?

Question

[Bioinf_Questions]

Hello. I'm making a heatmap of my data using heatmap.2, but once the plot is done there is no color scale. Shouldn't it be done automatically? What function should I use to put it in the plot?

Also, I'm getting the mesage "Error in plot.new() : figure margins too large". I used the function margins =c() to lower the margins so that the image isn't cut, but I still get the mesage. Do I need to change something or is there no problem even if I get that mesage?

Thanks in advance.

[antonioggsousa]

Hi,

I guess that the color scale is not appearing due to the error that you're getting "Error in plot.new() : figure margins too large", so its being cut. This is my guess since I just searched for that function and it seems that gives a color scale (see the link).

Which are the dimensions (rows x cols) of your matrix? (that you're providing to the function)

António

[Bioinf_Questions]

There are 4 columns and 50 rows.

[antonioggsousa]

I just tried on RStudio (v.2021.09.0 Build 351), with R version 4.1.2, gplots version 3.1.1, on Ubuntu 20.04.3 LTS, and it worked fine.

The dummy example that I used:

# Create fake matrix: 50 x 4
set.seed(1024)
m <- matrix(data = sample(100:1000, 200), ncol = 4)
row.names(m) <- paste0("row_", 1:nrow(m))
colnames(m) <- paste0("col_", 1:ncol(m))

# Import package 
library("gplots")

# Plotting heatmap
heatmap.2(m)

# Save heatmap
pdf("Desktop/heatmap.pdf", height=12) # you may adjust height
heatmap.2(m)
dev.off()

Perhaps try to avoid giving the margins option/function first to see if it works.

I guess that this also depends on how long are your label row names and col names.

I hope this helps,

António

[Bioinf_Questions]

Thank you very much.

[cpad0112]

are you using rstudio while plotting this?

[Bioinf_Questions]

Yes, I am.

[cpad0112]

One reason could be plot window (panel) is not big. Just drag the borders of plotting window to make it bigger.