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]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
T ++49/40/7410-58243
F ++49/40/7410-57790
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
