[BioC] RE: heatmap() column ordering

[Dave Waddell]

Oops, I take that back. The image is different now that I look at it more
closely (they are very similar). However, the original question remains -
how do I stop it from reordering the columns?
Dave.
-----Original Message-----
From: Dave Waddell [mailto:dwaddell at nutecsciences.com] 
Sent: Monday, November 03, 2003 9:54 AM
To: Bioconductor
Subject: heatmap() column ordering

I have four experiments (two dye swaps) and this is the original order:
> colnames(mav)
[1] Cy3="Cancer" Cy5="Normal" Cy3="Cancer" Cy5="Normal" Cy3="Normal"
Cy5="Cancer"Cy3=" Normal" Cy5="Cancer"

I want to get a heatmap of the top 30 expressed genes but ordered by
cancerous vs. normal tissue.
> hv <- heatmap(mav[genes %in% topgenes$Name,],col=RGcol)
> title("Heatmap of Top 30 genes")
> str(hv)
List of 2
 $ rowInd: int [1:30] 5 8 30 13 7 27 19 21 25 26 ...
 $ colInd: int [1:8] 4 3 8 7 1 5 2 6

No matter what I do, the columns are reordered. Furthermore, if I set Colv=F
the heatmap stays the same but the ordering changes.

> hv <- heatmap(mav[genes %in% topgenes$Name,],col=RGcol,Colv=F)
> title("Heatmap of Top 30 genes")
> str(hv)
List of 2
 $ rowInd: int [1:30] 5 8 30 13 7 27 19 21 25 26 ...
 $ colInd: int [1:8] 3 4 7 8 2 6 1 5

Am I missing something or is this a bug/feature?

BTW, is there any way to post images to this group? It seems this would be
desirable.
Dave Waddell