not sure about gplots, but the one in base R should work well if you
specify the scaling method to be 'none':
heatmap(a4[1:40, ], Rowv=NA, Colv=NA, col=c("grey", "blue", "purple",
"red"), scale='none')
Regards,
Yihui
--
Yihui Xie <xieyi...@gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Mon, Oct 24, 2011 at 6:07 PM, Weiwei Shi <helprh...@gmail.com> wrote:
> 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
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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