Mfuzz (version 2.32.0)

mfuzz.plot: 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

is color-encoded.

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)
}