\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}
 
   \item{title.add}{a title to add to the automatically
   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{plotDensOneAnnotInAllComp}} and
   \code{\link{qualVarAnalysis}} and is dedicated to the
   plot of the densities or boxplots using the package
   \code{\link{ggplot2}}.
 }
 \author{
   Anne Biton
 }
 \seealso{
   \code{\link[ggplot2]{geom_density}},
   \code{\link[ggplot2]{geom_boxplot}},
   \code{\link[ggplot2]{geom_point}}
 }
 \keyword{internal}