plotPosOneAnnotInComp_ggplot {MineICA} | R Documentation

## 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`

[Package MineICA version 1.26.0 Index]