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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