plot.segments {segmenTier}

Plot method for the "segments" object.

Description

plot the final segmentation objects returned by segmentClusters and segmentCluster.batch

Usage

## S3 method for class 'segments'
plot(x, plot = c("S", "segments"), types, params,
  xaxis, show.fused = FALSE, ...)

Arguments

x

a segmentation object as returned by segmentClusters and segmentCluster.batch

plot

string vector indicating which data should be plotted; "segments": plot segments as arrows; "S1" plot the scoring vectors s(i,j,c for all c; "S" plot the derivative of matrix S(i,c) for all c

types

a string vector indicating segment types to plot (a subset of x$ids; defaults to all in x$ids)

params

a named vector of parameter settings used in segmentCluster.batch allows to filter plotted segment types, e.g. params=c(S="icor") will only plot segments where the scoring function (parameter S) "icor" was used.

xaxis

optional x-values to use as x-axis (e.g. to reflect absolute chromosomal coordinates)

show.fused

show the fuse tag as a black x

...

additional arguments forwarded to arrows, eg. to set lwd for for plot="segments", or to matplot for plot="S"