Hi Sebastien.
My apologies, made a suggestion without running it myself. Try
something like:
qam <- QualityAssessmentModel(plm)
bpstats <- boxplotStats( getChipEffectSet(qam), type="RLE" )
# put in your specific arguments below ...
plotBoxplotStats(bpstats, boxwex=.2, boxfill=c("red","blue","green"))
Cheers,
Mark
On 04/02/2009, at 10:33 AM, Sebastien Gerega wrote:
>
> Hi Mark,
> thanks for your reply. I had actually tried several commands along
> those
> lines but always get the following:
> Error in boxplot.stats(theta - medianLE, ...) :
> unused argument(s) (boxwex = 0.4)
>
> or:
> Error in boxplot.stats(theta - medianLE, ...) :
> unused argument(s) (boxfill = "blue")
>
> The command works perfectly if I don't supply any additional
> arguments....
> thanks again,
> Sebastien
>
>
>
> Mark Robinson wrote:
>> Hi Sebastien.
>>
>> Note that plotRle() eventually makes a call to 'bxp' (in the graphics
>> package that is loaded by default) and any/all arguments are passed
>> on.
>> Have a look at ?bxp for what you can specify.
>>
>> For example:
>>
>> [...]
>> qamTr <- QualityAssessmentModel(plmTr)
>> plotRle(qamTr, boxwex=[something], boxfill=[something])
>>
>> Cheers,
>> Mark
>>
>>
>>> Hi,
>>> is there a way to change the colour of each individual bargraph when
>>> calling plotRle? I would like to make the colours correspond to test
>>> groups.
>>> thanks,
>>> Sebastien
>>>
>>>
>>>
>>
>>
>>
>>>
>>
>>
>
>
> >
------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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