matboxplot: Box plots of columns in a matrix

In quantro: A test for when to use quantile normalization

Description

Box plots of the columns of a matrix, but the columns are ordered and colored by a group-level variable

Usage

matboxplot(
  object,
  groupFactor,
  las = 3,
  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	a 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.
las	a numeric in (0, 1, 2, 3) to orient the axis labels. Default is 3 (always vertical).
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 codeboxplot function.

Value

A box plot for each column in object

Examples

library(minfi)
data(flowSorted)

p <- getBeta(flowSorted, offset = 100)
pd <- pData(flowSorted)
matboxplot(object = p, groupFactor = pd$CellType)

quantro documentation built on Nov. 8, 2020, 8:28 p.m.