Thanks guys, For the record I also found a nifty way to do this:

If genes are in rows and times in columns:
##########################
require(Mfuzz)
my.ts <- as.ts(t(my.gene.mat))
plot.ts(my.ts, plot.type = "single", main = "My time series")
##############################

Mark


On Mon, Mar 31, 2008 at 1:41 PM, Thomas Girke <thomas.girke@ucr.edu> wrote:

> Here is a simple example for generating line graphs for such data sets:
>
> # Generates a sample data set
> y <- as.data.frame(matrix(runif(30), ncol=3, dimnames=list(letters[1:10],
> LETTERS[1:3])))
>
> # Plots a line graph for all columns in data frame 'y'. The 'split.screen
> ()'
> # function is used in this example in a for loop to overlay several line
> graphs
> # in the same plot.
>
> plot(y[,1], type="l", lwd=2, col="blue") # Plots a line graph instead.
> split.screen(c(1,1))
> plot(y[,1], ylim=c(0,1), xlab="Measurement", ylab="Intensity", type="l",
> lwd=2, col=1)
>
> for(i in 2:length(y[1,])) {
>        screen(1, new=FALSE)
>        plot(y[,i], ylim=c(0,1), type="l", lwd=2, col=i, xaxt="n",
> yaxt="n", ylab="", xlab="", main="", bty="n")
> }
> close.screen(all=TRUE)
>
>
>
>
>
>
> On Mon 03/31/08 13:11, Mark Kimpel wrote:
> > In several papers I have seen a plot which illustrates the value of
> > expression of several genes (usually in a cluster) over time. The y axis
> is
> > expression, the x axis is discrete time points, and each of the points
> for a
> > gene are connected by lines so one can easily see a time profile.
> >
> > Is there a predefined function for this? If not, what plot parameters do
> I
> > use?
> >
> > Thanks,
> > Mark
> >
> > --
> > Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> > Indiana University School of Medicine
> >
> > 15032 Hunter Court, Westfield, IN  46074
> >
> > (317) 490-5129 Work, & Mobile & VoiceMail
> > (317) 663-0513 Home (no voice mail please)
> >
> > ******************************************************************
> >
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> >
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> >
>
> --
> Thomas Girke
> Assistant Professor of Bioinformatics
> Director, IIGB Bioinformatic Facility
> Center for Plant Cell Biology (CEPCEB)
> Institute for Integrative Genome Biology (IIGB)
> Department of Botany and Plant Sciences
> 1008 Noel T. Keen Hall
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke@ucr.edu
> Website: http://faculty.ucr.edu/~tgirke <http://faculty.ucr.edu/%7Etgirke>
> Ph: 951-827-2469
> Fax: 951-827-4437
>



-- 
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

******************************************************************

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