profileplot {bclust}R Documentation

a plot useful to visualise replicated data

Description

The profile plot is a flexible function creating profiles of replicated data with many useful options. The resulting plot can be attached to other plots like a horizontal dendrogram plot or a teethplot.

Usage

profileplot(x, rep.id, labels = NULL, scale = 1, col.names = colnames(x), 
plot.order = 1:max(rep.id), xlab.mar = 5, ylab.mar = 5, 
xlab.cex = 0.8, ylab.cex = 1, profile.col = rep(1, max(rep.id)), 
blob.matrix = matrix(0, ncol = ncol(x), nrow = max(rep.id)), 
blob.col = rev(heat.colors(max(blob.matrix))), blob.cex = 1.5)

Arguments

x The data matrix with subjects in rows and variables in columns.
rep.id A positive integer vector referring to replication of a subject such that the total number of subjects is max(rep.id).
labels The labels of each subject. The first element corresponds to the subject that takes value 1 in rep.id, the second element is the one that takes value 2 in rep.id and so on.
scale A positive value. If the profile plots are noisy or flat, adjust the scaling factor.
col.names The data column labels (variable labels) in a string vector.
plot.order A positive integer vector, the order that subjects should be plotted. This is useful if you like to attach this plot to a dendrogram or a teeth plot.
xlab.mar A positive value, the margin reserved for the column (variable) labels.
ylab.mar A positive value, the margin reserved for the subject labels.
xlab.cex A positive value, the magnitude of the variable labels.
ylab.cex A positive value, the magnitude of the subject labels.
profile.col Colours that you may used to plot each profile.
blob.matrix An integer matrix denoting where to plot a colour blob and which colour should be used in which location. The number of rows of this matrix should be max(rep.id) and the number of columns should be ncol(x). The value 0 plots no blobs, value 1 refers to plotting a blob with a colour specified in blob.col.
blob.col The colours that is used for each value of blob.matrix
blob.cex The magnitude of blobs.

Details

Some of the options may be useless for just a profile plot, but all of them are beneficial for a good visual representation of data when the plot is attached to a dendrogram or a teethplot.

See Also

teethplot, ditplot, dptplot.

Examples

data(gaelle)
#take a subset of gaelle data
subgaelle<-gaelle[1:11,]

#use thresholds to define blob colors
blob<-matrix(0,nrow(subgaelle),ncol(subgaelle))
blob[abs(subgaelle)<=0.74]<-0 
blob[abs(subgaelle)>0.74]<-1
blob[abs(subgaelle)>0.94]<-2
blob[abs(subgaelle)>1.28]<-3
profileplot(subgaelle,1:nrow(subgaelle),scale=10,blob.matrix=blob)

#make a profile plot with colored blobs
####### attach a profileplot to a teeth plot
subgaelle.bclust<-bclust(subgaelle,transformed.par=c(-1.84,-0.99,1.63,0.08,-0.16,-1.68))
# divide plot space into two unequal parts
layout(matrix(c(1,2),1,2,byrow=TRUE), c(9,1),10, respect=TRUE) 
# associate a color to each subject
subgaelle.color<-c(rep("blue",3),rep("green",4),rep("magenta",4))
# find appropriate order to plot subjects
subgaelle.order<-order.dendrogram(as.dendrogram(subgaelle.bclust))
#leave some space for labels 
x.mar<-7
y.mar<-5
profileplot(subgaelle,rep.id=1:nrow(subgaelle),scale=10,profile.col=subgaelle.color
,plot.order=subgaelle.order,xlab.mar=x.mar,ylab.mar=y.mar)
par(mar=c(x.mar,0,0,0))
teethplot(subgaelle.bclust)

####### nowattach it to a dendrogram plot
layout(matrix(c(2,1),1,2,byrow=TRUE), c(2,8),10, respect=TRUE) 
profileplot(subgaelle,rep.id=1:nrow(subgaelle),scale=10,profile.col=subgaelle.color
,plot.order=subgaelle.order,xlab.mar=x.mar,ylab.mar=y.mar)
par(mar=c(x.mar,0,0,0))
plot(as.dendrogram(subgaelle.bclust),horiz=TRUE,yaxs="i",axes=FALSE,leaflab="none")
abline(v=subgaelle.bclust$cut)

[Package bclust version 1.1 Index]