mfuzz.plot2: Plotting results for soft clustering with additional options
In Mfuzz: Soft clustering of time series gene expression data

Description Usage Arguments Value Author(s) Examples

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 `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`

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)




}

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

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Loading required package: e1071
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