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 classexprSet
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 1.6.0 Index]