mfuzz.plot2 {Mfuzz} | R Documentation |
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,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,...)
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. |
The function generates plots where the membership of genes is color-encoded.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
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) }