Plot expression profiles

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Description

Produces plots of clustered expression profiles, with seperate plots for each cluster. The average expression profile for each cluster is superimposed as well.

Usage

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clustPlot(cl, mat, nrow, ncol)

Arguments

cl

integer vector giving the cluster membership for each item

mat

matrix of values to be plotted

nrow

number of rows to use for plotting

ncol

number of columns to use for plotting

Details

The figure region will be subdivided into nrow by ncol separate plots, using mfrow. The average expression profile and the number of genes belonging to each cluster is superimposed on each of the plots.

References

G.N. Brock, V. Pihur, S. Datta, and S. Datta. clValid, an R package for cluster validation. Journal of Statistical Software, 25, 2008.

See Also

See the package vignette for illustration on usage

Examples

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## generate some fake data and cluster
set.seed(101)
mat <- matrix(rnorm(500), nrow=100, ncol=5)
clusts <- hclust(dist(mat))
cl <- cutree(clusts, 6)
clustPlot(cl, mat, 3, 2)