plotDens2classInComp_plotOnly {MineICA} | R Documentation

## Plots the densities or boxplots of the component contributions using `ggplot2`.

### Description

This internal function is called by `plotDensOneAnnotInAllComp` and `qualVarAnalysis` and is dedicated to the plot of the densities or boxplots using the package `ggplot2`.

### Usage

      plotDens2classInComp_plotOnly(annot, colAnnot, global,
        keepLev, comp.label = NULL, colours,
        legend.title = NULL, pval, test, title.add = NULL,
        data_ref = NULL, geneExpr = NULL, geneRef = NULL,
        ylab = NULL, trace_globalExpression = FALSE,
        trace_groupExpression = TRUE,
        typePlot = c("density", "boxplot"), addPoints = FALSE)

### Arguments

`annot` | a data.frame of dimensions 'samples x annotations' with one column corresponding to the component to trait ("comp" column) and one column corresponding to the groups of interest ("interest" column)
`colAnnot` | the name of a column of the argument `annot` with the groups of interest
`global` | a vector with the global distribution, e.g the contribution values of all samples on the component
`keepLev` | the groups of interest, i.e the levels of the annotation `colAnnot` to be considered
`comp.label` | the label of the component
`colours` | a vector of colours indexed by the names of the groups of interest
`legend.title` | the title of the legend, if NULL (default) colAnnot is used
`pval` | the p-value of the test, will be written in the title
`test` | name of test that gave the p-value
`title.add` | a title to add to the automatically generated title
`data_ref` | a data.frame similar to the argument `annot` but restricted to a set of reference samples
`geneExpr` | a vector of values representative of the component, e.g the expression of the witness gene of the component
`geneRef` | the ID of the feature/gene `geneExpr` corresponds to, e.g the name of the witness gene
`ylab` | A label for the y-axis (character)
`trace_globalExpression` | if TRUE, geneExpr is plotted below the graph as a set of points whose colour is representative of the amount of expression, default is FALSE
`trace_groupExpression` | if TRUE (default), geneExpr is plotted below the graph, by group, as a set of points whose colour is representative of the amount of expression
`typePlot` | The type of plot, either "density" or "boxplot"
`addPoints` | If TRUE, points are superimposed on the boxplots

### Value

A

### Author(s)

Anne Biton

### See Also

`geom_density`, `geom_boxplot`, `geom_point`

[Package MineICA version 1.24.0 Index]