[Bioc-devel] adding phenodata to heatmaps

Francois Pepin fpepin at cs.mcgill.ca
Mon Aug 28 18:25:14 CEST 2006

Hi everyone,

I was curious about what people thought of the issue of adding phenodata
(or other graphical components) under a heatmap.

Heatmap.2 allows for a single row of colors, and the Heatplus package
allows for several covariates, including plotting continuous values. I
ended up spending a couple of hours modifying heatmap.2 to do what I
wanted (before Seth pointed out to me that Heatplus existed).

Would it be worth it to make that functionality more visible (maybe
putting into heatmap/heatmap.2 or a function in ExpressionSet)? At this
point, adding any graphical component to a heatmap requires
understanding the whole layout code of the function which is not

I think it would be a good idea to increase its visibility and
accessibility, because it makes for much more readable figures for
people dealing with complex phenoData. Heatplus has the basic
functionality, but it does require some fiddling around to get 0/1
values for the phenoData (and they make some changes to where the sample
and gene names are placed).

I'd be happy to help a bit to get the functionality in if people think
it would be worth it.


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