[BioC] Colors in cColor from geneplotter

[Heidi Dvinge]

Dear all,

I want to use cPlot and cColor from the geneplotter package to  
visualise the intensity level of some genes from a microarray  
experiment on their given chromosomal location. However, I'm slightly  
confused by the results, especially since the colours don't really  
match what I get using alongChrom().

An example is shown below, using Entrez IDs. In this case I would  
expect the first probe in the "probes" argument to be associated with  
the first colour in "color" and so on, but that doesn't seem to be  
the case. At least not for my versions of the packages.

Any comments would be appreciated. Also, out of curiosity, what  
happens with those IDs that map to several locations within the  
genome, such as no. 19 and 64 in my xx list. Will the "color"  
argument automatically take that into consideration?

Thanks
\Heidi

library(geneplotter)
library(org.Mm.eg.db)
library(RColorBrewer)

# Test
x <- org.Mm.egCHRLOC
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
chr	<- buildChromLocation("org.Mm.eg.db")
cPlot(chr)
cColor(probes=names(xx[1:4]), color=c("red", "green", "blue",  
"purple"), plotChroms=chr)

# A (simplified) example similar to the vignette
dec	<- quantile(0:100, probs=seq(0,1,0.1))
class	<- cut(1:100, dec)
col	<- brewer.pal(10, "RdYlGn")
cPlot(chr)
cColor(probes=names(xx[1:100]), color=col[class], plotChroms=chr)


sessionInfo()
R version 2.7.0 Patched (2008-05-18 r45723)
i386-apple-darwin8.10.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets   
methods   base

other attached packages:
  [1] RColorBrewer_1.0-2  org.Mm.eg.db_2.2.0  geneplotter_1.18.0   
annotate_1.18.0     xtable_1.5-2
  [6] AnnotationDbi_1.2.0 RSQLite_0.6-8       DBI_0.2-4            
lattice_0.17-7      Biobase_2.0.1

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22 grid_2.7.0