profileplot {bclust} | R Documentation |
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.
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)
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 |
labels |
The labels of each subject. The first element corresponds to the subject that takes value 1 in |
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 |
blob.col |
The colours that is used for each value of |
blob.cex |
The magnitude of blobs. |
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.
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)