\name{plotPosAnnotInComp}
\alias{plotPosAnnotInComp}
\title{Histograms of sample contributions for each annotation level}
\usage{
plotPosAnnotInComp(icaSet, params,
keepVar = varLabels(icaSet),
keepComp = indComp(icaSet),
keepSamples = sampleNames(icaSet), pathPlot = NULL,
breaks = 20, colAll = "grey74", colSel, resClus,
funClus = c("Mclust", "kmeans"), nbClus = 2,
by = c("annot", "component"),
typeImage = c("pdf", "png", "none"), ...)
}
\arguments{
\item{icaSet}{An object of class \code{IcaSet}}

\item{params}{A \code{MineICAParams} object}

\item{keepVar}{The variable labels to be considered, i.e
a subset of the column labels of the pheno data of icaSet
available in (\code{varLabels(icaSet)})}

\item{keepComp}{A subset of components available in
\code{indComp(icaSet)}; by default, all components are
used}

\item{keepSamples}{A subset of samples, must be available
in \code{sampleNames(icaSet)}; by default, all samples
are used}

\item{pathPlot}{A character specifying the path where the
plots will be saved}

\item{breaks}{The number of breaks to be used in the
histograms}

\item{colSel}{The colour of the histogram of the group of
interest, default is "red"}

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

\item{resClus}{A list containing the outputs of function
\code{clusterSamplesByComp}, which consists of sample
clustering applied to matrix A of argument \code{icaSet}.
If missing, the clustering is performed by the function.}

\item{funClus}{The clustering method to be used, either
\code{"Mclust"} or \code{"kmeans"}. If \code{resClus} is
not missing, equals \code{resClus\$funClus}.}

\item{nbClus}{If \code{resClus} is missing, it provides
the number of clusters to be computed by \code{funClus},
default is 2}

\item{by}{Either \code{"annot"} to plot the histograms of
each variable across all components, or
\code{"component"} to plot the histograms for each
component across variables. When \code{by="annot"} one
pdf file is created by variable name, while when
\code{annot="component"}, one pdf file is created by
component.}

\item{typeImage}{The type of image to be created, either
"pdf" (default) or "png". "png" is not recommended,
unless there are at the most 4 histograms to be plotted,
because it does not allow to deal with multiple pages of
plots.}

}
\value{
NULL
}
\description{
This function plots the positions of groups of samples
formed by the variables (i.e the sample annotations)
across all the components of an object of class
variable level (e.g for each tumor stage) this function
plots the positions of the corresponding samples (e.g the
subset of samples having this tumor stage) within the
histogram of the global sample contributions. The plots
are saved in pdf file, one file is created per variable.
The pdf files are names 'variable.pdf' and save either in
\code{pathPlot} if specified or the current directory.
}
\details{
The plotted values are the sample contributions across
the components, i.e across the columns of
\code{A(icaSet)}.

If argument \code{resClus} is missing, the function
computes the clustering of the samples on each component
(i.e on each column of \code{A(icaSet)}) using
\code{funClus} and \code{nbClus}.

The association between the clusters and the considered
sample group is tested using a chi-square test. The
p-values of these tests are available in the title of
each plot.

When \code{by="annot"} this function plots the histograms
of each variable across all components, to plot the
histograms for each component across variables, please
use \code{by="component"}.
}
\examples{
\dontrun{
## load an example of IcaSet
data(icaSetCarbayo)

## Use icaSetCarbayo, look at the available annotations
varLabels(icaSetCarbayo)

## Plot positions of samples in components according to annotations 'SEX' and 'STAGE'
# plots are saved in files SEX.pdf and STAGE.pdf created in the current directory
plotPosAnnotInComp(icaSet=icaSetCarbayo, keepVar=c("SEX","STAGE"), keepComp=1:2,  funClus="Mclust")
# specifiy arg 'pathPlot' to save the pdf in another directory, but make sure it exists before
# specifiy arg 'by="comp"' to create one pdf file per component
}
}
\author{
Anne Biton
}
\seealso{