Anne Biton authored on 23/04/2020 18:30:14
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\code{names(samplesByGroup)} is NULL.}
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\item{icaSet}{An object of class
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- \code{\link[MineICA:IcaSet-class]{IcaSet}}}
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+ \code{\link[MineICA:class-IcaSet]{IcaSet}}}
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\item{keepComp}{A subset of components available in
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\code{indComp(icaSet)}, if NULL (default) all components
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@@ -57,7 +57,7 @@ |
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\description{
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This function plots the positions of several groups of |
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samples across all the components of an |
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- \code{\link[MineICA:IcaSet-class]{icaSet}} object.
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+ \code{\link[MineICA:class-IcaSet]{icaSet}} object.
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} |
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\details{
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For each subgroup of samples this function plots their |
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@@ -98,7 +98,7 @@ dev.off() |
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} |
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\seealso{
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\code{\link{hist}},
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- \code{\link[MineICA:IcaSet-class]{IcaSet}}
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+ \code{\link[MineICA:class-IcaSet]{IcaSet}}
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} |
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\keyword{internal}
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 05/02/2013 22:15:53
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new file mode 100644 |
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+\name{plotPosSamplesInComp}
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+\alias{plotPosSamplesInComp}
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+\title{Histograms of sample subsets}
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+\usage{
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+ plotPosSamplesInComp(samplesByGroup, labGroups = NULL, |
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+ icaSet, keepComp = indComp(icaSet), file = NULL, |
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+ breaks = 20, colAll = "grey74", colSel = "red", |
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+ titlesup = "", resClus, |
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+ funClus = c("Mclust", "kmeans"), ...)
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+} |
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+\arguments{
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+ \item{samplesByGroup}{A list whose elements are vector of
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+ sample names, these sample names must be available in |
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+ \code{sampleNames(icaSet)}. The list should be indexed by
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+ the name of the corresponding groups.} |
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+ |
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+ \item{labGroups}{A vector of group names, will be used to
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+ add names to \code{sampleByGroup} if
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+ \code{names(samplesByGroup)} is NULL.}
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+ |
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+ \item{icaSet}{An object of class
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+ \code{\link[MineICA:IcaSet-class]{IcaSet}}}
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+ |
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+ \item{keepComp}{A subset of components available in
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+ \code{indComp(icaSet)}, if NULL (default) all components
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+ are used} |
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+ |
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+ \item{file}{A pdf file}
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+ |
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+ \item{breaks}{The number of breaks to be used in the
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+ histograms} |
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+ |
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+ \item{colSel}{The colour of the histogram of the group of
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+ interest, default is "red"} |
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+ |
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+ \item{colAll}{The colour of the global histogram, default
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+ is "grey74"} |
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+ |
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+ \item{resClus}{A list containing the outputs of function
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+ \code{\link{clusterSamplesByComp}}, which consists of
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+ results of clustering applied to matrix A of argument |
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+ \code{icaSet}.}
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+ |
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+ \item{funClus}{Specifies the clustering method used,
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+ either \code{"Mclust"} or \code{"kmeans"}. If
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+ \code{resClus} is not missing, equals
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+ \code{resClus$funClus}.}
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+ |
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+ \item{titlesup}{Additional title for the histograms}
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+ |
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+ \item{...}{Additional parameters for function
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+ \code{\link{hist}}}
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+} |
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+\value{
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+ NULL |
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+} |
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+\description{
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+ This function plots the positions of several groups of |
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+ samples across all the components of an |
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+ \code{\link[MineICA:IcaSet-class]{icaSet}} object.
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+} |
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+\details{
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+ For each subgroup of samples this function plots their |
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+ positions within the histogram of the global sample |
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+ contributions. |
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+ |
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+ The values of interest are the sample contributions |
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+ across the components, i.e across the columns |
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+ \code{A(icaSet)}.
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+ |
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+ If argument \code{resClus} is not missing, the
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+ association between the clusters and the sub-groups of |
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+ samples is tested using a chi-square test. The p-values |
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+ of these tests are available in the title of each plot. |
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+} |
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+\examples{
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+\dontrun{
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+## load an example of IcaSet |
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+data(icaSetCarbayo) |
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+ |
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+## selection of sample groups according to annotations STAGE |
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+samplesByGroup <- lapply(split(pData(icaSetCarbayo),pData(icaSetCarbayo)[c("STAGE")]), rownames)
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+# select groups including at least 2 samples |
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+samplesByGroup <- samplesByGroup[which(unlist(lapply(samplesByGroup,length))>1)] |
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+ |
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+## clustering of samples according to A using Mclust imposing two Gaussian |
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+resClus <- clusterSamplesByComp(icaSet=icaSetCarbayo,funClus="Mclust", nbClus=2, clusterOn="A") |
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+ |
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+## Plot positions of the groups in 5th component |
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+pdf(file="stageOnIC5.pdf", height = 8.267717, width = 29.7/2.54, paper = 'a4r', title="stageOnIC5") |
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+plotPosSamplesInComp(samplesByGroup=samplesByGroup, icaSet=icaSetCarbayo, funClus="Mclust", |
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+ resClus = resClus, keepComp=5) |
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+dev.off() |
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+} |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+\seealso{
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+ \code{\link{hist}},
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+ \code{\link[MineICA:IcaSet-class]{IcaSet}}
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+} |
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+\keyword{internal}
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+ |