Heatmap/Color Selection(Key)

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Hi Rashid,
you may have a look at the colorRampPalette-function, along with the
"at" argument oh heatmap.2

x<-matrix(runif(100,-6,6),nrow=10)
heatmap.2(x,col=colorRampPalette(c("blue","lightblue","darkgray","darkgray","yellow","red"),space="Lab"),at=c(-6.01,6.01,51))
# or just using the colors you posted
heatmap.2(x,col=c("blue","lightblue","darkgray","black","darkgray","yellow","red"),at=-3:3*2)

hth.

Am 08.10.2010 17:03, schrieb rashid kazmi:
Hi
I made heatmap of QTL based on Lod score. Where I have traits in columns and
marker data (rows). I can not cluster both column and rows as I need the
right order for marker data.

Can someone suggest me better way of generating heatmaps especially the
colour key I want to select to visualize the results which are more
interesting to look at.

library(gplots)

sample=read.csv(file.choose())

sample.names<-sample[,1]

sample.set<-sample[,-1]

sample.map <- as.matrix(sample.set)

### have to order as i have markers on rows so just want denrogram on
triats(column)

ord <- order(rowSums(abs(sample.map)),decreasing=T)

heatmap.2(sample.map[ord,],Rowv=F,dendrogram="column",trace="none",col=greenred(10))

But I want to give colours more specifically as I want to show the QTL
hotspots starting as fallow

1)      -6  to -4 (blue)

2)       -4 to -2 (light blue)

3)      -2 to  0  (dark grey or black)

4)      0 to 2 (dark grey or black)

5)      2 to 4 (yellow)

6)      4 to 6 (red)

Any help or some addition to the above mentioned R code would be
appreciated.

R Kazmi

PhD

The Netheralnd

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sorry, typo:
heatmap.2(x,col=colorRampPalette(c("blue","lightblue","darkgray","darkgray","yellow","red"),space="Lab"),at=c(-6.01,6.01,51))
heatmap.2(x,col=c("blue","lightblue","darkgray","black","darkgray","yellow","red"),at=-3:3*2)
should be read as

heatmap.2(x,col=colorRampPalette(c("blue","lightblue","darkgray","darkgray","yellow","red")),breaks=seq(-6.01,6.01,length.out=51))
heatmap.2(x,col=c("blue","lightblue","darkgray","darkgray","yellow","red"),breaks=-3:3*2)

"at" from stats:heatmap became "breaks" in gplots:heatmap.2