Visualisation of cluster overlap and global clustering structure

Description

This function visualises the cluster overlap produced by overlap.

Usage

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overlap.plot(cl,overlap,thres=0.1,scale=TRUE,magni=30,P=NULL)

Arguments

cl

object of class “flclust”

overlap

matrix of cluster overlap produced by overlap

thres

threshold for visualisation. Cluster overlaps below the threshold will not be visualised.

scale

Scale parameter for principal component analysis by prcomp

magni

Factor for increase the line width for cluster overlap.

P

Projection matrix produced by principal component analysis.

Value

A plot is genererated based on a prinicpal component analysis of the cluster centers. The overlap is visualised by lines with variable width indicating the strength of the overlap. Additonally, the matrix of principal components is returned. This matrix can be re-used for other projections to compare the overlap and global cluster structure of different clusterings.

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

See Also

prcomp

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
cl <- mfuzz(yeastF,c=20,m=1.25)
X11();mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))
O <- overlap(cl)
X11();Ptmp <- overlap.plot(cl,over=O,thres=0.05)

# Alternative clustering 
cl <- mfuzz(yeastF,c=10,m=1.25)
X11();mfuzz.plot(yeastF,cl=cl,mfrow=c(3,4))
O <- overlap(cl)

X11();overlap.plot(cl,over=O,P=Ptmp,thres=0.05)
# visualisation based on  principal compents from previous projection
}

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