[BioC] Heatmap quick questions

[James W. MacDonald]

Hi Daniel,

Daniel Brewer wrote:
> Hi,
> 
> A few quick questions about heatmap that I could not find via google or
> the newsgroup search:
> 1) How can you change the font size of the row labels?  At the moment
> they are merging.

Use the cexRow argument.

> 2) Is there a simple way to have the top row of the matrix at the top of
> the picture rather than the other way round?

I assume you are setting Rowv=NA to keep from reordering? If so, you can 
just use heatmap(yourmatrix[dim(matrix)[1]:1,], otherargs).

If you are not setting Rowv=NA, then the row ordering is dictated by the 
hierarchical clustering of the genes. I suppose you could cluster the 
genes first, then reorder the HC result the way you want (assuming that 
you are simply inverting the order), and then feed that as the argument 
to Rowv.

> 3) Is there a way to make the blocks square?

Technically, yes. Just use the right number of genes ;-D

The graphics gurus might have a fix, but as it stands R tries to fit the 
graphics within the available plotting region, so the blocks will get 
flattened as much as necessary to make things fit. If you really want 
the heatmap to have square blocks (and just get longer), then you might 
want to use Mike Eisen's Cluster/Treeview software.

Best,

Jim


> 
> Many thanks
> 
> Daniel
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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