mfuzz.plot {Mfuzz}R Documentation

Plotting results for soft clustering

Description

This function visualises the clusters produced by mfuzz.

Usage

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://itb.biologie.hu-berlin.de/~futschik)

Examples

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)
}

[Package Mfuzz version 1.12.0 Index]