spectralMap-methods: Methods for Function spectralMap according to JnJ Standards

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Methods for spectralMap

Usage

## S4 method for signature 'ExpressionSet,character'
spectralMap(
  object,
  groups,
  makeLognormal = TRUE,
  mpm.args = list(row.weight = "mean", col.weight = "constant", logtrans = TRUE),
  plot.mpm.args = list(zoom = c(1, 2), label.tol = 10, rot = c(-1, 1), sub = "",
    lab.size = 0.85, col.group = pData(object)[, groups], colors = c("wheat", "darkgrey",
    a4palette(nlevels(pData(object)[, groups]))), col.size = 2, do.smoothScatter = TRUE),
  probe2gene = TRUE,
  addLegend = TRUE,
  legendPos = "topleft",
  ...
)

Arguments

object	object of class ExpressionSet
groups	string indicating the name of the column in the phenoData that defines the groups
makeLognormal	boolean indicating whether one wants to exponentiate the data to make them lognormally shaped (TRUE; the default) or not (FALSE)
mpm.args	list of arguments that can be passed to the mpm function
plot.mpm.args	list of arguments that can be passed to the plot.mpm function that actually draws the plot
probe2gene	boolean indicating whether one wants to display the gene symbols for the labeled points (TRUE) or not (FALSE; the default)
addLegend	Boolean indicating whether a legend for the colors of the dots should be added.
legendPos	Specify where the legend should be placed. Typically either topright,
...	further arguments to be passed to the methods, currently not used.

Value

the plot is returned invisibly

Author(s)

Tobias Verbeke

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.