R help - Oct 2012 - Reading labels for very large heatmaps

Hello,
I have a large (919 X 919), hierarchically clustered heatmap that I would
like to read the labels off of.  I have tried saving the figure in pdf
format and enlarging it until I can see the labels, but if I make the labels
small enough to read (so that they don't overlap) using cexRow and cexCol,
they do not appear in the pdf.  The limit seems to be anything below cexRow
or Col = 0.06.  Is there a way to have smaller labels visible in the pdf? 
Is this an issue with resolution?  I could get by with just a quarter of the
heatmap (i.e. half of a row and half of a column) so that the labels don't
have to be so small, but the heatmap must be clustered before this is done. 
I tried to cut the dendrogram at just the halfway point of the heatmap, but
was not successful.  Any suggestions?
Thanks,
Jacob



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Jacob,

Try increasing the size of the pdf.  For example, I can read all 919 
labels in this plot ...

pdf(width=200, height=200)
plot(1:919, 1:919, axes=FALSE)
axis(1)
axis(2, at=1:919, las=1, cex=0.01)
box()
graphics.off()

Jean



JIMonroe <jim5bm@virginia.edu> wrote on 10/01/2012 03:42:24
PM:
> 
> Hello,
> I have a large (919 X 919), hierarchically clustered heatmap that I 
would
> like to read the labels off of.  I have tried saving the figure in pdf
> format and enlarging it until I can see the labels, but if I make the 
labels
> small enough to read (so that they don't overlap) using cexRow and 
cexCol,
> they do not appear in the pdf.  The limit seems to be anything below 
cexRow
> or Col = 0.06.  Is there a way to have smaller labels visible in the 
pdf? 
> Is this an issue with resolution?  I could get by with just a quarter of 
the
> heatmap (i.e. half of a row and half of a column) so that the labels 
don't
> have to be so small, but the heatmap must be clustered before this is 
done. 
> I tried to cut the dendrogram at just the halfway point of the heatmap, 
but
> was not successful.  Any suggestions?
> Thanks,
> Jacob
	[[alternative HTML version deleted]]

Jean,

It's definitely bigger now, but my axes are cut-off.  As in your example, I
had them drawn after generating the heatmap, but the image does not seem to
be centered.  I think even part of the heatmap is getting cut off, which
wasn't happening until I explicitly set the width and height of the pdf. 
Here is my code
> pdf("Apo_Mut_Boot.pdf", width=200, height=200)
> heatmap(x=as.matrix((Apo_Mut)), col >
colorRampPalette(c("white","black"))(256),
> zlim=c(min(Apo_Mut),max(Apo_Mut)),    add = FALSE, xaxs = "i",
yaxs > "i",xaxt= "n", yaxt = "n",
xlab="residue", ylab="residue",
> main="Apo-Mutant",revC=TRUE, Rowv = as.dendrogram(blah2), Colv
> as.dendrogram(blah2), reorderfun = function(d,w) rev(reorder(d,w)),
> oldstyle = FALSE,cexRow=0.01,cexCol=0.01,symm=TRUE )
> axis(1, at=1:919, labels=RowCol, las=2, cex=0.01)
> axis(4, at=1:919, labels=RowCol, las=2, cex=0.01)
> box()
> graphics.off()
Jacob



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