R programming - Graphic edges too large error while using clustering.plot in EMA package

Question

I'm an R programming beginner and I'm trying to implement the clustering.plot method available in R package EMA. My clustering works fine and I can see the results populated as well. However, when I try to generate a heat map using clustering.plot, it gives me an error "Error in plot.new (): graphic edges too large". My code below,

#Loading library
library(EMA)
library(colonCA)

#Some information about the data
data(colonCA)
summary(colonCA)
class(colonCA) #Expression set

#Extract expression matrix from colonCA
expr_mat <- exprs(colonCA)

#Applying average linkage clustering on colonCA data using Pearson correlation
expr_genes <- genes.selection(expr_mat, thres.num=100)
expr_sample <- clustering(expr_mat[expr_genes,],metric = "pearson",method = "average")
expr_gene <- clustering(data = t(expr_mat[expr_genes,]),metric = "pearson",method =   "average")
expr_clust <- clustering.plot(tree = expr_sample,tree.sup=expr_gene,data=expr_mat[expr_genes,],title = "Heat map of clustering",trim.heatmap =1)

I do not get any error when it comes to actually executing the clustering process. Could someone help?

Answer 1

In your example, some of the rownames of expr_mat are very long ( max(nchar(rownames(expr_mat)) = 271 characters). The clustering_plot function tries to make a margin large enough for all the names but because the names are so long, there isn't room for anything else.

The really long names seem to have long stretches of periods in them. One way to condense the names of these genes is to replace runs of 2 or more periods with just one, so I would add in this line

#Extract expression matrix from colonCA
expr_mat <- exprs(colonCA)
rownames(expr_mat)<-gsub("\\.{2,}","\\.", rownames(expr_mat))

Then you can run all the other commands and plot like normal.