RnBeads (version 1.4.0)

rnb.plot.betadistribution.probeCategories: rnb.plot.betadistribution.probeCategories

Description

plot beta value distrubions given probe categories

Usage

rnb.plot.betadistribution.probeCategories(beta.matrix, probe.cat, annotation = "Group", color.legend = NULL, log.str = NULL, points.per.group = rnb.getOption("distribution.subsample"))

Arguments

beta.matrix

Beta values in the form of a non-empty matrix of type double. Rows in this matrix must correspond to Infinium probes, and columns - to samples.

probe.cat

factor vector of length nrow(beta.matrix) corresponding to the probe categories.

annotation

Name of the annotation being visualized, in the form of a character vector of length 1.

color.legend

Color legend to use in the form of a character vector with element names. The values in this vector should encode colors. All values in probe.cat must be present in the names of this color legend. If this parameter is NULL, a default color legend is be constructed.

log.str

string specifying more details for the log file

points.per.group

the targeted number of points per group. Set this to a value < 1 to disable subsampling. More information in the Details section of rnb.step.betadistribution

Value

The plot as a ggplot2 object.

See Also

rnb.plot.betadistribution.sampleGroups

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
meth.mat <- meth(rnb.set.example)
probe.types <- annotation(rnb.set.example)[, "Design"]
rnb.plot.betadistribution.probeCategories(meth.mat,probe.types,annotation="Infinium probe type")