[R] Questions about 'heatmap.2' function

From: karena <dr.jzhou_at_gmail.com>
Date: Tue, 26 Apr 2011 13:06:34 -0700 (PDT)


I am trying a heatmap.

I have 30 individuals and 1,000 genes.

Some components I want for this heatmap plot: (1) the 'color-key'; (2) a banner across the top to emphasize how the hierarchical clustering has correctly split the data into the two groups;

I use the 'heatmap.2' function in the 'gplots' package, and my function is as below:



jpeg('/plots/heatmap.jpg')
heatmap.2(data, scale="column", key=TRUE, trace="none", xlab="individuals", ylab="genes", main="heatmap", density.info="histogram", col=redblue) dev.off()

I have two problems now:
1) I don't know how to use the 'ColSideColors' option to emphasize the 'groups' rather than 'each individuals'. 2) When I only included 100 genes in my heatmap, I had no problems getting the 'color-key'; However, when I included more genes (i.e., 300 genes), I can NOT get the 'color-key' any more, even that all the options are exactly the same), and the error message I got is :

"Error in image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, :
  breaks must all be finite"

Can anyone help me on this?

thank you very much!

karena

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Received on Tue 26 Apr 2011 - 20:23:54 GMT

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