R help - Oct 2010 - Heatmap/Color Selection(Key)

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

	[[alternative HTML version deleted]]

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
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Eik Vettorazzi
Institut f?r Medizinische Biometrie und Epidemiologie
Universit?tsklinikum Hamburg-Eppendorf

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20246 Hamburg

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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