[R] Questions about 'heatmap.2' function

karena dr.jzhou at gmail.com
Tue Apr 26 22:06:34 CEST 2011

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:
heatmap.2(data, scale="column", key=TRUE, trace="none", xlab="individuals",
ylab="genes", main="heatmap", density.info="histogram", col=redblue)
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!


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