\name{plotDens2classInComp_plotOnly}
\alias{plotDens2classInComp_plotOnly}
\title{Plots the densities or boxplots of the component contributions using \code{\link{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{
\item{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)}

\item{colAnnot}{the name of a column of the argument
\code{annot} with the groups of interest}

\item{global}{a vector with the global distribution, e.g
the contribution values of all samples on the component}

\item{keepLev}{the groups of interest, i.e the levels of
the annotation \code{colAnnot} to be considered}

\item{comp.label}{the label of the component}

\item{colours}{a vector of colours indexed by the names
of the groups of interest}

\item{legend.title}{the title of the legend, if NULL
(default) colAnnot is used}

\item{pval}{the p-value of the test, will be written in
the title}

\item{test}{name of test that gave the p-value}

generated title}

\item{data_ref}{a data.frame similar to the argument
\code{annot} but restricted to a set of reference
samples}

\item{geneExpr}{a vector of values representative of the
component, e.g the expression of the witness gene of the
component}

\item{geneRef}{the ID of the feature/gene \code{geneExpr}
corresponds to, e.g the name of the witness gene}

\item{ylab}{A label for the y-axis (character)}

\item{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}

\item{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}

\item{typePlot}{The type of plot, either "density" or
"boxplot"}

\item{addPoints}{If TRUE, points are superimposed on the
boxplots}
}
\value{
A
}
\description{
This internal function is called by
\code{\link{qualVarAnalysis}} and is dedicated to the
plot of the densities or boxplots using the package