Plotting results for soft clustering

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Description

This function visualises the clusters produced by mfuzz.

Usage

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mfuzz.plot(eset,cl,mfrow=c(1,1),colo,min.mem=0,time.labels,new.window=TRUE)

Arguments

eset

object of the classExpressionSet.

cl

object of class flclust.

mfrow

determines splitting of graphic window.

colo

color palette to be used for plotting. If the color argument remains empty, the default palette is used.

min.mem

Genes with membership values below min.mem will not be displayed.

time.labels

labels can be given for the time axis.

new.window

should a new window be opened for graphics.

Value

The function generates plots where the membership of genes is color-encoded.

Author(s)

Matthias E. Futschik (http://www.sysbiolab.eu/matthias)

Examples

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if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)

# Soft clustering and visualisation
cl <- mfuzz(yeastF,c=20,m=1.25)
mfuzz.plot(yeastF,cl=cl,mfrow=c(2,2))

# display of cluster cores with alpha = 0.5
mfuzz.plot(yeastF,cl=cl,mfrow=c(2,2),min.mem=0.5)

# display of cluster cores with alpha = 0.7
mfuzz.plot(yeastF,cl=cl,mfrow=c(2,2),min.mem=0.7)
}

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