overlap.plot: Visualisation of cluster overlap and global clustering...

In Mfuzz: Soft clustering of time series gene expression data

Description

This function visualises the cluster overlap produced by overlap.

Usage

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

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
}

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: e1071
Warning message:
no DISPLAY variable so Tk is not available 

Mfuzz documentation built on Nov. 8, 2020, 5:22 p.m.