title: R figure being cropped
body: <p>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:</p>
  
  <p><a href="https://i.stack.imgur.com/ToFXi.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/ToFXi.png" alt="there&#39;s supposed to be five numbers after the final letter of the labels"></a></p>
  
  <p>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.</p>
  
  <p><strong>EDIT:</strong> Procedure to reproduce this visualisation:</p>
  
  <p>Input data:</p>
  
  <pre><code>Time,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48
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  CATMA5A25890,-0.23072,0.82252,0.32512,0.13284,0.14406,0.005071,0.40953,-0.11252,-0.6367,-0.048073,0.21325,-0.046316,-0.35078,1.1023,-0.019882,-0.55825,-0.34621,0.1114,0.030302,-0.08142,0.19157,0.5152,-0.034952,0.20984,1.0547,0.4816,0.31078,0.14731,0.31811,-0.27275,-0.47217,-0.043207,0.29109,0.41192,-1.069,0.23357,-0.17453,0.015661,-0.26869,0.14587,0.19336,0.5926,-0.1583,0.61242,0.18635,0.01207,-0.21772,0.13986,1.9305,0.3349,0.62954,-0.04455,1.121,-0.14155,-0.33772,-0.42633,0.41828,-0.29794,-0.7107,1.4786,-0.37442,-0.45371,0.16175,-0.057764,-0.11803,-0.037838,0.25868,0.88605,0.33225,-0.24331,0.93084,-0.33266,0.9762,0.24755,0.30857,0.14661,1.8351,0.40313,0.45084,-0.52105,-0.31271,-0.37122,-0.28615,-0.0023692,-0.43072,-0.24417,-0.5184,0.13874,-0.32606,-0.1705,2.1396,-0.77657,2.3056,0.32096,0.29337,-0.034746
  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></pre>
  
  <p>Code proper (BHC is from Bioconductor):</p>
  
  <pre><code>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)) &lt;- this fixes it on a single-case basis
  dev.off()
  </code></pre>