Thanks Mark,
that takes care of changing the colours but for some reason the names
argument still isn't influencing anything. For example:
bpstats = boxplotStats(getChipEffectSet(qam), type="NUSE")
plotBoxplotStats(bpstats, boxfill=c("red","blue","green"), names=c("G1",
"G2", "G3"))
does not change the names displayed under the boxplots. Any idea how to
change this?
thanks again,
Sebastien
Mark Robinson wrote:
> 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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