Starr (version 1.28.0)

plotProfiles: Plotting ChIP profiles of one or more clusters

Description

plotProfiles plots the ChIP profiles of one or more clusters. Additionally on can display the distribution of e.g. gene expression in the clusters.

Usage

plotProfiles(profiles, mfcol=NULL, mfrow=NULL, ylab="intensity", xlab="position", histograms=NULL, cluster, profileplot=T, meanprofile=T, ...)

Arguments

profiles

a list constructed by the function getProfiles().

mfcol

see ?par

mfrow

see ?par

ylab

see ?par

xlab

see ?par

histograms

a list of named vectors. Density plots are created for every vector and cluster.

cluster

A named integer vector, that maps the features to the cluster.

profileplot

should a clusterplot be shown?

meanprofile

should the mean profiles of each cluster be plotted??

...

arguments, passed to plot.default

See Also

density, profileplot

Examples

## 
sampls = 100
probes = 63
clus = matrix(rnorm(probes*sampls,sd=1),ncol=probes)
clus= rbind( t(t(clus)+sin(1:probes/10))+1:nrow(clus)/sampls , t(t(clus)+sin(pi/2+1:probes/10))+1:nrow(clus)/sampls )
clustering = kmeans(clus,3)$cluster
names(clustering) <- 1:length(clustering)


profiles <- apply(clus, 1, function(x) {list(upstream=x[1:20], region=x[21:43], downstream=x[44:63])})
names(profiles) <- 1:length(clustering)
profiles <- list(profile=profiles, upstream=20, downstream=20, borderNames=c("start", "stop"))

plotProfiles(profiles, cluster=clustering, ylim=c(-1,2.5), type="l", lwd=2)