[BioC] Multiple colours in GenomeGraphs?

James Bullard bullard at berkeley.edu
Thu May 22 19:22:48 CEST 2008

Hi Mark,

Colors are handled somewhat differently at this point depending on  
what class you are in (i.e. BaseTrack, GenericArray).

dp1 = DisplayPars(color = c(rep("blue", 1), rep("red", 1)))
dp2 = DisplayPars(color = c(rep("blue", 500), rep("red", 500)))

gdPlot(new("BaseTrack", base = rpois(1000, 1), value =  
exp(rnorm(1000)), dp = dp1))
gdPlot(new("BaseTrack", base = rpois(1000, 1), value =  
exp(rnorm(1000)), dp = dp2))

For the generic array:

gdPlot(new("GenericArray", probeStart = rpois(1000, 1), intensity =  
matrix(exp(rnorm(2000)), ncol = 2), dp = dp1))

Note: here are coloring is based on which column it is. So if I use my  
dp2 in this case I don't really get anything sensible. In this case  
colors pertain to columns and not individual points. Please let me  
know what class your using and I can probably add the capability to do  
what you want. Features like this we definitely want to support, we  
just haven't got around to ironing them out.

thanks, jim

On May 15, 2008, at 7:39 AM, Mark Dunning wrote:

> Hi all,
> I have just started using the GenomeGraphs package, which I think is a
> really good piece of software :)
> I am using the package to plot expression values across a genomic
> region. However, it seems to plot all points on the same "track" in  
> the
> same colour? I was wondering if it is possible to use different  
> colours
> to highlight particular probes I am interesting in, (or use different
> plotting characters). I thought something like:
> dp=DisplayPars(color=c("red","blue")) might work, but it just produced
> one colour. Apologies if there is already the ability to do this,  
> but I
> didn't see anything so far.
> Many thanks,
> Mark
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