[BioC] Fine tuning heatmap.2 graphics

[Marc Saric]

Dear all,

I like to use heatmap.2 from the gplots library package to automatically
plot heatmaps from microarray data.

Things work fine so far, but two problems remain:

1. Depending on the amount of data to be displayed, the fontsize of the
labels changes dynamically (as it should) and with that, the
margin-space required to print the labels changes also (leading to
truncated labels sometimes).

This can be set manually with

margin <- c(x,y);

for both x and y axis labels margins.

Is there an easy way to compute the required margin size dynamically
from -say- the lenght of the longest label-string?


2. Plotting with heatmap.2 in the X11 device gives a plot, in which all
the coloured rectangles are drawn without visible separating border
between them.

When plotting as "pngalpha" with the bitmap device, you can see
separating bright borderlines, which -due to the antialiasing- are only
partly visible (i.e. some lines are there, some have been removed by the
antialiasing).

Is there any option to remove this borders when plotting with bitmap and
"pngalpha"?

I have tried with

sepwidth = c(0.0,0.0),
sepcolor = "black",

but this does not have any visible effect.

Thanks in advance.

-- 
Bye,

Marc Saric