[BioC] DNA copy ploting function

[Nathalie Conte]

HI,
I am using DNAcopy package (http://prs.ism.ac.jp/bioc/2.7/bioc/html/DNAcopy.html) in order to plot my agilent CGHarrays (mouse):(chromosome in X axis and logR in Y axis)

I have 2 questions about this package:
I have done the data segmentation using the segment () function and now I want to plot my data using plot() from DNA copy, there is an option to plot all genom  in one plot ( "w" option)
example : plot(segment.smoothed.CNA.object, plot.type = "w")
question 1: the chromosomes alternate in different colours and are sorted in this order: 1 then 10 then 11, 12, 13 ,14 ,15, 16, 17 ,18 ,19 ,2 ,3 ,4, 5 ,6 ,7 ,8 ,9, I would rather have them in the natural order: 1,2,3,4.....Is there an easy way to change the plot order?

Question2: Is it possible at this point to plot the probe using a colour that will correspond to their log2R, example if a probe log2R is more than 0.2 plot it in red??


thanks
Nat



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