heatmap for plotting categorical matrix

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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