[R] Issues with Heat Map Images

[David Winsemius]

On Nov 8, 2012, at 7:58 AM, cpleisner wrote:

> David,
> Thanks for the help.  I tried the following code:
> 
> heatdata <- read.csv("logFC_bin17.csv", sep=",")
> heatdata <- heatdata[,2:5]
> heatdata_matrix <- data.matrix(heatdata)
> rownames(heatdata_matrix) = paste("Gene", 2:655)
> jpeg("Heatmap_bin17.jpeg", width=8, height=8, units="in", res=300, 
> quality=100) 
> data_heatmap <- heatmap.2(heatdata_matrix, col=redblue(75), scale="row", 
> key=TRUE, symkey=FALSE, density.info="none", trace="none", margins=c(10,10), 
> cexRow=0.5) 
> axis(4, 
>      at=1:NROW(heatdata_matrix), 
>      labels=rownames(heatdata_matrix[data_heatmap$rowInd] ), 
>      cex=0.5) 
> dev.off() 
> 
> It solved the issue with the jpeg, but I am still getting the following
> image:
> <http://r.789695.n4.nabble.com/file/n4648906/Heatmap_bin17.jpeg> 

I suspect that the labels are in that smeared black band on the RHS of the plot. You should consider plotting this with pdf() and zooming in to see if you even need an extra axis call.


> 
> The axis labels are still off and now there is this '1' in the upper right
> hand corner.  Thoughts?

-- 
David Winsemius, MD
Alameda, CA, USA