plotPosOneAnnotInComp_ggplot: Tests if groups of samples are differently distributed on the...

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

Tests if groups of samples are differently distributed on the components and do the corresponding plots.

Description

Given a variable of the phenoData, this function tests if the groups of samples formed by this variable are differently distributed, in terms of contribution value (i.e of values in matrix A(icaSet)), on the components. The distribution of the groups on the components are represented using density plots. It is possible to restrict the tests and the plots to a subset of samples and/or components.

Usage

  plotPosOneAnnotInComp_ggplot(icaSet, params, colAnnot,
    keepLev = NULL, keepComp, samples, colAll = "grey74",
    binwidth = 0.1, addExpr = TRUE, file = NULL, ...)

Arguments

icaSet	An object of class IcaSet
params	An object of the class MineICAParams containing the parameters of the analysis
colAnnot	a variable label, i.e one of the variables available in (varLabels(icaSet)) containing the groups of interest
samples	a subset of sample names available in samplenames(icaSet), if NULL (default) all samples are used
keepComp	a subset of components available in indComp(icaSet), if NULL (default) all components are used
keepLev	the groups of interest, i.e the levels of the variable colAnnot to be considered
colAll	The colour of the global histogram, default is "grey74"
file	the file where the histograms will be plotted
addExpr	if TRUE (default) the expression profiles of the witness genes of each component are added below the plot
binwidth	binwidth of the histogram (default is 0.1)
...	other parameters for geom_histogram function from ggplot2 package

Details

Wilcoxon or Kruskal-Wallis tests are applied depending on the number of groups of interest from the considered annotation (argument keepLev). One png image is created by plot and located in path. Each image is named by component-of-component_colAnnot.png.

Value

NULL

Author(s)

Anne Biton

See Also

plotPosOneAnnotLevInComp_ggplot, geom_histogram

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.