Plotting results for soft clustering with additional options
This function visualises the clusters
produced by mfuzz. it is similar to mfuzz.plot, but offers
more options for adjusting the plots.
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,...)eset |
object of the classExpressionSet. |
cl |
object of class flclust. |
mfrow |
determines splitting of graphic window. Use
|
colo |
color palette to be used for plotting. If the
color argument remains empty, the default palette is
used. If the |
min.mem |
Genes with membership values below
|
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 |
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 |
The function generates plots where the membership of genes is color-encoded.
Matthias E. Futschik (http://www.sysbiolab.eu/matthias)
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)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.