Visualisation of cluster overlap and global clustering structure
This function visualises the cluster overlap
produced by overlap.
overlap.plot(cl,overlap,thres=0.1,scale=TRUE,magni=30,P=NULL)
cl |
object of class “flclust” |
overlap |
matrix of cluster overlap produced by |
thres |
threshold for visualisation. Cluster overlaps below the threshold will not be visualised. |
scale |
Scale parameter for principal component
analysis by |
magni |
Factor for increase the line width for cluster overlap. |
P |
Projection matrix produced by principal component analysis. |
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.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
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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