On 11/03/2010 02:50 AM, Hua wrote:
...
When I try to make heatmap based on this gene expression value table, I found
that, when I set 'scale' to 'column', the heatmap will be always be red. I
think this is because, there's very large values in the matrix (gene Actb),
while the most are just very small. Thus, the color will be very ugly. I just
wonder, how to set the color to make the heatmap look better? I have tried
log-tranformation on the matrix and it's better now. But I do want to know if
you have better ways to set the color span manually and make the heatmap look
better without any log-transformation?
Hi Hua,
It is not all that easy, but can be done. I read in your data as
"genexp". Notice how I split up the data into three ranges, adding the
range extremes in color.scale (plotrix) and then removing the extremes.
expcol[genexp$sample2<100]<-
color.scale(c(0,100,genexp$sample2[genexp$sample2<100]),
c(1,0.5),c(0,0.5),0)[-(1:2)]
expcol[genexp$sample2>=100&genexp$sample2<1000]<-
color.scale(c(100,1000,genexp$sample2[genexp$sample2>=100&genexp$sample2<1000]),
c(0.5,0.1),c(0.5,0.9),0)[-(1:2)]
expcol[genexp$sample2>1000]<-
color.scale(c(1000,10000,genexp$sample2[genexp$sample2>=1000]),
c(0.1,0),c(0.9,1),0)[-(1:2)]
barplot(rep(1,27),col=expcol)
color.legend(0,-0.1,15,-0.05,c(0,100,1000,10000),
rect.col=c("red","#808000","#1ae600","green"))
Jim
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