plotProfiles {Starr} | R Documentation

## 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

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### 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)

[Package Starr version 1.36.0 Index]