image.splitSet: Illustrate Split Sets

Description

Draws an image of all splits, one per row, of a splitSet object. Each column corresponds to a patient.

Usage

"image"(x, filter.fdr = 1, main = "", max.label.length = 50,  full.names = TRUE, xlab = NULL, sample.labels = FALSE,  col = c("yellow", "red"), invert = FALSE,  outfile = NULL, res = 72, pointsize = 7, ...)

Arguments

the object of class splitSet to be illustrated.

filter.fdr

worst acceptable false discovery rate for the shown set of splits. All splits with q-values below this level are dropped from the image.

main

a title for the image.

max.label.length

Maximal length of the annotations shown to the right of the image. Longer annotations are truncated.

full.names

Show full names for annotations instead of their identifiers only.

xlab

additional annotation on the x-axis.

sample.labels

whether names of samples are to be shown on the x-axis.

col

two strings encoding the colors to be used to illustrate to which group a sample is attributed.

invert

whether to draw in white on black background.

outfile

the filename on which to draw the image in postscript format. The default is NULL, meaning to produce the image interactively.

res

resolution for bitmap output on postscript.

pointsize

size of font.

...

further arguments passed to image.

Value

Always returns NULL.

Details

The set of splits given is illustrated as an image. Each row corresponds to an annotation, each column to a patient. In position (x,y), the association of patient x to a group with respect to annotation y is coded as colors (yellow and red by default). The image is ordered by hierarchical clustering such that similar patients and similar splits are brought closer together.

Examples

Run this code

data(golubKEGGSplits)
image(golubKEGGSplits, filter.fdr=0.5)