checkerboard {globaltest}R Documentation

Checkerboard plot for Global Test

Description

Produces a plot to visualize the test result produced by globaltest, by showing the association between pairs of samples.

Usage

checkerboard(gt, geneset, sort = TRUE, drawlabels = TRUE, 
labelsize = 0.6, ...)

Arguments

gt The output of a call to globaltest.
geneset The name or number of the geneset to be plotted (only necessary if multiple genesets were tested)
sort A logical flag to indicate whether the samples should be sorted by the clinical outcome to give a clearer picture.
drawlabels Logical value to control drawing of the samplenames on the x- and y-axis of the plot.
labelsize Relative size of the labels on the x- and y-axis. If it is NULL , the current value for par("cex.axis") is used
... Any extra arguments will be forwarded to the plotting function.

Details

The checkerboard shows the pairs of samples which have high covariance in white and the pairs with low covariance in black. This can be used to visualize the data and to search for outlying arrays.

The left and bottom margins are adjusted to allow enough space for the longest samplename.

Value

A matrix giving the old and the new sample numbers.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

References

J. J. Goeman, S. A. van de Geer, F. de Kort and J. C. van Houwelingen, 2004, A global test for groups of genes: testing association with a clinical outcome, Bioinformatics 20 (1) 93–99. See also the How To Globaltest.pdf included with this package.

See Also

globaltest, sampleplot, geneplot.

Examples

    data(exampleX)      # Expression data (40 samples; 1000 genes)
    data(exampleY)      # Clinical outcome for the 40 samples
    pathway <- 1:25     # A pathway contains genes 1 to 25
    
    gt <- globaltest(exampleX, exampleY, test.genes = pathway)
    gt
    
    if (interactive()) {
      checkerboard(gt)
    }

[Package globaltest version 3.2.0 Index]