[BioC] Point plot against labels and reordering

[Daniel Brewer]

Thanks James and Sean, using a combination of the two that worked great.
> matplot(monkey[c(6,7,2,8,9,10,11,3,12,13,4,5,1),2:4], xaxt="n")
>
axis(side=1,at=1:nrow(monkey),labels=as.character(monkey$Exon[c(6,7,2,8,9,10,11,3,12,13,4,5,1)]),las=2)

Excellant.

Dan

James W. MacDonald wrote:
> Hi Dan,
> 
> Daniel Brewer wrote:
>> Hi,
>>
>> I am getting really frustrated with trying to create a specific plot.  I
>> have the following matrix (monkey):
>>     Exon      PRC1     PRC2     PRC3
>> 1  0_110 2.0132845 1.484080 1.923869
>> 2   0_34 2.6528139 1.141114 1.242584
>> 3   0_78 1.6247146 1.230726 1.592407
>> 4     10 1.4471323 1.137777 1.426656
>> 5     11 1.5471201 1.204736 1.500566
>> 6      2 1.0423570 1.104883 1.087180
>> 7      3 0.9563367 1.017354 1.067159
>> 8      4 1.4577586 1.166938 1.422878
>> 9      5 1.5081813 1.177205 1.494983
>> 10     6 1.4432391 1.144851 1.396613
>> 11     7 1.6995243 1.337146 1.643418
>> 12     8 1.3848549 1.096389 1.357165
>> 13     9 1.4995867 1.162944 1.444809
>>
>> Exon is the Exon number of a label saying which two exons the probe is
>> in-between.  That column should be treated as labels, not numeric.
>>
>> What I would like to be able to do is plot for example PRC1 on the
>> y-axis and the Exon as the x-axis labels (just evenly spaced not a
>> numeric scale).  Secondly I would like to be able to reorder the labels
>> for the plot.
>>
>> The closest I have got is:
>> plot(monkey$Exon,monkey$PRC1)
> 
> Does
> 
> plot(1:dim(monkey)[1], monkey$PRC1, xaxt="n")
> axis(1, at=1:dim(monkey)[1], labels = monkey$Exon, las=2)
> 
> do what you want?
> 
> Best,
> 
> Jim
> 
>     
>>
>> But that seems to be producing a boxplot rather than points.  If I put
>> type="p" it makes no difference and if I try and reorder the matrix it
>> does not make any difference either e.g.
>> monkey$Exon[c(6,7,2,8,9,10,11,3,12,13,4,5,1)]
>>
>> monkey$Exon is a factor object
>>
>> Any help would be great.
>>
>> Dan
>>
> 
> 

-- 
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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