Plotting results for soft clustering with additional options

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Description

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

Usage

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mfuzz.plot2(eset,cl,mfrow=c(1,1),colo,min.mem=0,time.labels,time.points,
ylim.set=c(0,0), xlab="Time",ylab="Expression changes",x11=TRUE,
                        ax.col="black",bg = "white",col.axis="black",col.lab="black",
                        col.main="black",col.sub="black",col="black",centre=FALSE,
                        centre.col="black",centre.lwd=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 for ticks on x axis.

time.points

numerical values for the ticks on x axis. These can be used if the measured time points are not equidistant.

ylim.set

Vector of min. and max. y-value set for plotting. If ylim.set=c(0,0), min. and max. value will be determined automatically.

xlab

label for x axis

ylab

label for y axis

x11

If TRUE, a new window will be open for plotting.

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.

centre

If TRUE, a line for the cluster centre will be drawn.

centre.col

Color of the line for the cluster centre

centre.lwd

Width of the line for the cluster centre

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 and axes functions such as cex.lab,cex.main,cex.axis

Value

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

Author(s)

Matthias E. Futschik (http://www.sysbiolab.eu/matthias)

Examples

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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
mfuzz.plot2(yeastF, cl=cl,mfrow=c(2,2),centre=TRUE) # lines for cluster centres will be included

# 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=1.3,cex.lab=1.1)

### 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)


### Single cluster  with colorbar (cluster # 3
X11(width=14)
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",time.labels = c(paste(seq(0,160,10),"min")),
col.main="green",col.sub="blue",col="blue",cex.main=2, single=3,x11=FALSE)

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




}

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