Hi there,

I have a matrix like this:

> a4[1:20, 1:5]
           194 211 294 314 315
GO:0000003   1   1   1   1   1
GO:0000072   0   0   0   0   0
GO:0000076   1   0   0   0   0
GO:0000082   1   3   1   1   1
GO:0000083   1   0   0   0   1
GO:0000086   0   1   0   1   1
GO:0000114   0   0   0   0   0
GO:0000115   0   0   0   0   0
GO:0000117   0   0   0   0   0
GO:0000160   0   0   1   0   0
GO:0000212   0   0   0   0   0
GO:0000216   1   0   0   1   0
GO:0000226   1   0   1   0   0
GO:0000278   1   1   1   2   1
GO:0000320   0   0   0   0   0
GO:0000710   0   0   0   0   0
GO:0000768   0   0   0   0   0
GO:0000819   1   0   0   1   1
GO:0000910   1   0   0   3   0
GO:0000917   0   0   0   0   0

I wanted to plot a heatmap to assign "grey" to 0, "blue" to 1, "purple" to
2, and "red" to 3. I did not some trials and found some problems like this:

When the row is all zero, there could be a white bar in the middle of the
heatmap though I did not assign "white" to any value.

Or some row believes "grey" as 0 while some rows believes "blue" as "0".

Did I make some mistake here?

library(gplots)

heatmap.2(a4[1:40,],  Rowv=NA, Colv=NA, col=c("grey", "blue", "purple",
"red"), trace="none")


Thanks,

Weiwei
-- 
Weiwei Shi, Ph.D
Research Scientist


"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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