plotDens2classInComp_plotOnly: Plots the densities or boxplots of the component...

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

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

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