[BioC] Situation of the legend in the plotPCA of the affycoretools library

[James W. MacDonald]

Hi Jordi,

Jordi Altirriba Gutiérrez wrote:
> Dear BioC users,
> I am trying to do a PCA plot with the package affycoretools, which I have 
> found very useful!
> I am not able to change the situation of the legend in the plot, although I 
> have introduced the variables x.coord and y.coord in the script. Could it be 
> a little bug or am I doing something wrong?
>   

No bug, just a misunderstanding. There are no arguments x.coord or 
y.coord (actually, I don't think these are arguments for any plotting 
function that I can think of - where did you get the idea you could pass 
these as arguments?).

Anyway, the function is set up to automagically place the legend in one 
of the corners of the plot based on having space for the legend to fit, 
and if there isn't space in a corner, to ask the end user where to put 
it. I suppose I could modify the function to accept a legend location if 
there is a good reason to override the automatic placement.

Best,

Jim


> Many thanks in advance!
>
> This is my code:
> library(affycoretools)
> Data<-ReadAffy()
> eset<-rma(Data)
> pd <- read.phenoData("pdata2.txt", header = TRUE, row.names = 1)
> plotPCA(eset,groups = rep(1:2, each = 3), groupnames = 
> unique(pData(pd))[,1],addtext=sampleNames(Data))
>
> I obtain exactly the same plot writing:
> plotPCA(eset,groups = rep(1:2, each = 3), groupnames = 
> unique(pData(pd))[,1],addtext=sampleNames(Data),x.coord=0,y.coord=0)
>
> My session:
>   
>> sessionInfo()
>>     
> Version 2.3.1 (2006-06-01)
> i386-pc-mingw32
>
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
>
> other attached packages:
>    rat2302cdf affycoretools       GOstats      Category      hgu95av2
>      "1.12.0"       "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"
>          KEGG      multtest    genefilter      survival        xtable
>      "1.12.0"      "1.10.2"      "1.10.1"        "2.28"       "1.3-2"
>          RBGL      annotate            GO         graph         Ruuid
>       "1.8.1"      "1.10.0"      "1.12.0"      "1.10.6"      "1.10.0"
>         limma          affy        affyio       Biobase
>      "2.7.10"      "1.10.0"       "1.0.0"      "1.10.1"
>
> Jordi Altirriba
> PhD student
> Hospital Clinic (Barcelona, Spain)
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>   

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623



**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.