plotPosOneAnnotInComp_ggplot: Tests if groups of samples are differently distributed on the...
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Details Value Author(s) See Also

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.

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

`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

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.

NULL

Anne Biton

plotPosOneAnnotLevInComp_ggplot, geom_histogram

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.