\name{plotPosOneAnnotInComp_ggplot}
\alias{plotPosOneAnnotInComp_ggplot}
\title{Tests if groups of samples are differently distributed on the components and do the corresponding plots.}
\usage{
plotPosOneAnnotInComp_ggplot(icaSet, params, colAnnot,
keepLev = NULL, keepComp, samples, colAll = "grey74",
binwidth = 0.1, addExpr = TRUE, file = NULL, ...)
}
\arguments{
\item{icaSet}{An object of class \code{IcaSet}}

\item{params}{An object of the class \code{MineICAParams}
containing the parameters of the analysis}

\item{colAnnot}{a variable label, i.e one of the
variables available in (\code{varLabels(icaSet)})
containing the groups of interest}

\item{samples}{a subset of sample names available in
\code{samplenames(icaSet)}, if NULL (default) all samples
are used}

\item{keepComp}{a subset of components available in
\code{indComp(icaSet)}, if NULL (default) all components
are used}

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

\item{colAll}{The colour of the global histogram, default
is "grey74"}

\item{file}{the file where the histograms will be
plotted}

\item{addExpr}{if TRUE (default) the expression profiles
of the witness genes of each component are added below
the plot}

\item{binwidth}{binwidth of the histogram (default is
0.1)}

\item{...}{other parameters for geom_histogram function
from ggplot2 package}
}
\value{
NULL
}
\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 \code{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.
}
\details{
Wilcoxon or Kruskal-Wallis tests are applied depending on
the number of groups of interest from the considered
annotation (argument \code{keepLev}). One png image is
created by plot and located in \code{path}. Each image is
named by component-of-component_colAnnot.png.
}
\author{
Anne Biton
}
\seealso{