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quantro (version 1.6.2)

matdensity: Density plots of columns in a matrix

Description

Plots the density of the columns of a matrix

Usage

matdensity(object, groupFactor = NULL, type = "l", lty = 1,
  brewer.n = 8, brewer.name = "Dark2", ...)

Arguments

object
object an object which is inherited from an eSet such as an ExpressionSet or MethylSet object. The object can also be a data frame or matrix with observations (e.g. probes or genes) on the rows and samples as the columns.
groupFactor
an optional factor variable representing which group each column in object belongs to. It is important that values in groupFactor be in the same order as the columns in object.
type
the type of lines to plot. Default type is line ("l").
lty
the line type. Default is the solid line.
brewer.n
the number of colors in the palette from the RColorBrewer package. Default is 8.
brewer.name
the name of the palette from the RColorBrewer package. Default is "Dark2".
...
other arguments that can be passed to the code{matplot} function.

Value

  • A density plot for each column in object

Examples

Run this code
library(minfi)
data(flowSorted)
p <- getBeta(flowSorted, offset = 100)
pd <- pData(flowSorted)
matdensity(object = p, groupFactor = pd$CellType, xlab = "beta values",
ylab = "density")

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