mfuzz.plot2 {Mfuzz}R Documentation

Plotting results for soft clustering with additional options

Description

This function visualises the clusters produced by mfuzz. it is similar to mfuzz.plot, but offers more options for adjusting the plots.

Usage

mfuzz.plot2(eset,cl,mfrow=c(1,1),colo,min.mem=0,time.labels,x11=TRUE,
                        ax.col="black",bg = "white",col.axis="black",col.lab="black",
                        col.main="black",col.sub="black",col="black",cex.main=2,
                        Xwidth=5,Xheight=5,single=FALSE,...)

Arguments

eset object of the classExpressionSet.
cl object of class flclust.
mfrow determines splitting of graphic window. Use mfrow=NA if layout is used (see example).
colo color palette to be used for plotting. If the color argument remains empty, the default palette is used. If the colo = "fancy", an alternative (fancier) palette will be used.
min.mem Genes with membership values below min.mem will not be displayed.
time.labels labels can be given for the time axis.
x11
ax.col Color of axis line.
bg Background color.
col.axis Color for axis annotation.
col.lab Color for axis labels.
col.main Color for main titles.
col.sub Color for sub-titles.
col Default plotting color.
cex.main Magnification to be used for main titles.
Xwidth Width of window.
Xheight Height of window.
single Integer if a specific cluster is to be plotted, otherwise it should be set to FALSE.
... Additional, optional plotting arguments passed to plot.default function.

Value

The function generates plots where the membership of genes is color-encoded.

Author(s)

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

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.plot2(yeastF,cl=cl,mfrow=c(2,2)) # same output as mfuzz.plot

# More fancy choice of colors
mfuzz.plot2(yeastF,cl=cl,mfrow=c(2,2),colo="fancy",
ax.col="red",bg = "black",col.axis="red",col.lab="white",
col.main="green",col.sub="blue",col="blue",cex.main=2)

### Single cluster  with colorbar (cluster # 3) 
X11(width=12)
mat <- matrix(1:2,ncol=2,nrow=1,byrow=TRUE)
l   <- layout(mat,width=c(5,1))
mfuzz.plot2(yeastF,cl=cl,mfrow=NA,colo="fancy", ax.col="red",bg = "black",col.axis="red",col.lab="white",
col.main="green",col.sub="blue",col="blue",cex.main=2, single=3,x11=FALSE)

mfuzzColorBar(col="fancy",main="Membership",cex.main=1)
}

[Package Mfuzz version 1.12.0 Index]