R help - Mar 2008 - Adding name labels to x-axis of matplot

Hello,

I have a gene expression matrix with columns being samples and rows
being genes.  I would like to display the expression values for each
gene.  I have two groups which I colour differently.  The aim is to see
if there is any difference between the two groups consistently across genes.

So the following works well:

matplot(as.matrix(nonormexpr),pch=16,col=c(rep(1,length(left)),rep(2,length(right))),cex=0.4)

The only thing is that the x-axis has numbers 1 ... 10, whereas I would
like to give them the names of the genes.  I have tried using the
"labels" parameter but I get:

Error in axis(side, at, as.graphicsAnnot(labels), tick, line, pos,
outer,  :
        'labels' is supplied and not 'at'

Any ideas?  Is there are a more appropriate plot type?

-- 
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
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.

This e-mail message is confidential and for use by the a...{{dropped:2}}

try this:

dat <- matrix(rnorm(20), 10, 2)
dimnames(dat) <- list(1:10, c("sample1", "sample2"))

matplot(dat, pch = 16, xaxt = "n", col = 1:2,
    ylab = "Expression Value")
axis(1, at = 1:10, labels = paste("Gene", 1:10), cex.axis = 0.7)


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Daniel Brewer" <daniel.brewer at icr.ac.uk>
To: <r-help at stat.math.ethz.ch>
Sent: Wednesday, March 26, 2008 12:10 PM
Subject: [R] Adding name labels to x-axis of matplot

> Hello,
>
> I have a gene expression matrix with columns being samples and rows
> being genes.  I would like to display the expression values for each
> gene.  I have two groups which I colour differently.  The aim is to 
> see
> if there is any difference between the two groups consistently 
> across genes.
>
> So the following works well:
>
>
matplot(as.matrix(nonormexpr),pch=16,col=c(rep(1,length(left)),rep(2,length(right))),cex=0.4)
>
> The only thing is that the x-axis has numbers 1 ... 10, whereas I 
> would
> like to give them the names of the genes.  I have tried using the
> "labels" parameter but I get:
>
> Error in axis(side, at, as.graphicsAnnot(labels), tick, line, pos,
> outer,  :
>        'labels' is supplied and not 'at'
>
> Any ideas?  Is there are a more appropriate plot type?
>
> -- 
> **************************************************************
> Daniel Brewer, Ph.D.
> Institute of Cancer Research
> Molecular Carcinogenesis
> 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.
>
> This e-mail message is confidential and for use by the...{{dropped:14}}