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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