Extra heatmap.2 arguments

[adomingues]

First of all thank you @lishen for this very useful package. I have one suggestion which I think would improve it further. Whilst the plots generated via drawHeatmap are good enough for internal presentations, the visualization could be improved for papers/presentations. For instance the labels are quite large in relation to the cells. Would it be possible to pass extra arguments to heatmap.2 in the function?

I am thinking something along the lines of:

setMethod(
    "drawHeatmap", "GeneOverlapMatrix",
    function(object, what=c("odds.ratio", "Jaccard"), log.scale=F, adj.p=F, 
             cutoff=.05, ncolused=9, grid.col=c("Greens", "Blues", "Greys", 
                                                "Oranges", "Purples", "Reds"),
note.col="red",
... # other arguments to be passed on to heatmap.2
) {
# (..)

heatmap.2(plot.mat, cellnote=note.mat, ...)

This would increase the flexibility of visualization immensely.

I guess the only other alternative would be for the user to extract the values using getMatrix(object) and then construct the plot from scratch.

Cheers.

[adomingues]

Hi @lishen,

I wonder if you had a chance of looking into this issue.

Cheers,
António