\name{plotDensOneAnnotInAllComp}
\alias{plotDensOneAnnotInAllComp}
\title{Tests if groups of samples are differently distributed on the components and do the corresponding plots.}
\usage{
plotDensOneAnnotInAllComp(icaSet, keepVar, path = NULL,
samples, keepComp, keepLev = NULL, colours = NULL,
legend.title = NULL, doPlot = TRUE, cutoff = 0.05,
onlySign = TRUE, resTests)
}
\arguments{
\item{icaSet}{an object of class

\item{keepVar}{a variable label, i.e the label of a
column of the pheno data of icaSet available in
(\code{varLabels(icaSet)}) wich contains the groups of
interest}

\item{path}{the directory where the plots will be
located}

\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 annotation \code{keepVar} to be considered}

\item{colours}{A vector of colours indexed by the
elements of \code{keepLev}, if NULL the colours are
generated automatically using annot2Color}

\item{legend.title}{title of the legend}

\item{cutoff}{The threshold p-value for statistical
significance}

\item{doPlot}{if TRUE (default), the plots are drawn,
else if FALSE only test results are returned}

\item{onlySign}{if TRUE (default), only the significant
results are plotted}

\item{resTests}{a vector of p-values per component, if
NULL (default) the p-values are calculated using Wilcoxon
or Kruskal-Wallis test}
}
\value{
Returns a data.frame of dimensions 'components x 1'
containing the results of the non-parametric tests
(Wilcoxon or Kruskal-Wallis tests) that test if the
groups of interest are differently distributed on the
components
}
\description{
Given a variable of the phenotype data (i.e vector of
sample annotations), this function tests if the groups of
samples formed by this variable are differently
distributed on the components, in terms of contribution
values. 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}). The plots are saved
in individual files (one file per component) in arg
'path' if specified or in the current directory if not
specificied. Ech individual file is nameb
'index-of-component_colAnnot.png.' Recall that the
sample-contribution values are contained in
\code{A(icaSet)}, and the sample annotations in
\code{pData(icaSet)}.

One png image is created by plot and located in
\code{path}. Each image is named by
'index-of-component_keepVar.png'.
}
\examples{
\dontrun{
## load an example of IcaSet
data(icaSetCarbayo)

## have a look at the sample annotations which are available
varLabels(icaSetCarbayo)

## with doPlot=TRUE trace the contributions of the samples according
## to their grade on the components
doPlot=FALSE)
}
}
\author{
Anne Biton
}
\seealso{
}
\keyword{internal}