[BioC] plot multiple genes over time

Thomas Girke thomas.girke at ucr.edu
Mon Mar 31 19:41:33 CEST 2008

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.
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") 

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
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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 at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437

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