mfuzz.plot: Plotting results for soft clustering

In Mfuzz: Soft clustering of time series gene expression data

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://www.sysbiolab.eu/matthias)

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)
}

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.