R figure being cropped

Question

Here's a bit of a basic question, you'd think R would automate this always. I'm making a heatmap (basic stuff, png() into heatmap.2() into dev.off()), and my row labels get cleaved off on the right hand side, along with a tiny part of the dendrogram on the left:

Fiddling with the margins manually would eventually lead to a sensible output, but the problem is that this is part of an automated pipeline with biologist users in mind. Surely there's some automated way to do this, right? I mean, in RGui on OSX, a quick reshape of the figure window fixes the layout automatically, so it has to be possible. Thanks, and sorry to bother you.

EDIT: Procedure to reproduce this visualisation:

Input data:

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CATMA5A31940,4.4307,4.8735,4.7911,5.8201,5.9587,5.576,5.9084,5.849,5.2832,5.5423,5.0275,4.5254,4.5054,3.0696,5.6512,4.3986,4.9856,4.9222,4.951,4.5506,4.2185,4.3184,5.4783,4.4515,3.9397,5.6269,5.0988,6.1254,5.7446,5.6146,5.452,5.2047,5.3527,5.93,4.8931,5.5529,3.9876,4.1072,4.0583,5.4324,5.4681,4.392,4.5189,5.0629,4.9347,5.2165,4.6681,4.7428,4.1539,6.3376,5.353,6.2896,5.5844,5.1654,5.4391,5.3933,5.261,5.6974,4.5142,3.9851,3.569,4.0946,4.6662,5.1085,5.0319,4.4598,4.8672,3.7326,5.3032,5.0448,4.7771,4.2209,4.1886,4.284,5.4681,5.8331,4.7683,5.6614,5.3313,5.2017,5.1002,5.0642,4.4867,4.8576,4.1454,4.0971,5.0368,4.845,4.753,5.5496,2.9838,5.1394,3.342,4.1246,5.0121,4.618

Code proper (BHC is from Bioconductor):

library(argparse)
library(RColorBrewer)
library(BHC)
library(parallel)
library(gplots)

#data prep and clustering, to get dendrograms etc as shown in plot
data = read.csv('input.csv',header=TRUE,row.names=1,check.names=FALSE)
genes = rownames(data)
samples = colnames(data)
data = data.matrix(data)
standardisedData = (data-mean(data))/sd(data)
samples = as.numeric(samples)
hc = bhc(standardisedData, genes, timePoints=samples, dataType='time-course', verbose=TRUE)

#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'))
#heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(3,10)) <- this fixes it on a single-case basis
dev.off()

Answer 1

I would suggest just giving it a fairly wide default margin, such that it should be clipped even with longer labels, e.g.:

heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(14, 14))

The default margin size is (5,5). The above increases the both the column and row margins, but you can increase just one or the other as well.

If you want to be more precise, you could try using max(strwidth(rownames(standardisedData))) to determine the amount of space needed by the largest label, and then convert that into the units expected by par(mar=*) (what heatmap.2() uses to specify plot margins.)

I think this should do the trick:

# determine margins to use
png('/tmp/trash', width=6,height=6,units='in',res=300)
plot.new()
margin_width = max(strwidth(rownames(standardisedData), units='inches')) * par('fin')[1]
dev.off()

#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(5, margin_width))
dev.off()