Anne Biton authored on 23/04/2020 18:30:14
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This function plots the positions of groups of samples |
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formed by the variables (i.e the sample annotations) |
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across all the components of an object of class |
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- \code{\link[MineICA:IcaSet-class]{icaSet}}. For each
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+ \code{\link[MineICA:class-IcaSet]{icaSet}}. For each
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variable level (e.g for each tumor stage) this function |
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plots the positions of the corresponding samples (e.g the |
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subset of samples having this tumor stage) within the |
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{plotPosAnnotInComp}
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+\alias{plotPosAnnotInComp}
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+\title{Histograms of sample contributions for each annotation level}
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+\usage{
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+ plotPosAnnotInComp(icaSet, params, |
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+ keepVar = varLabels(icaSet), |
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+ keepComp = indComp(icaSet), |
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+ keepSamples = sampleNames(icaSet), pathPlot = NULL, |
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+ breaks = 20, colAll = "grey74", colSel, resClus, |
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+ funClus = c("Mclust", "kmeans"), nbClus = 2,
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+ by = c("annot", "component"),
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+ typeImage = c("pdf", "png", "none"), ...)
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+} |
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+\arguments{
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+ \item{icaSet}{An object of class \code{IcaSet}}
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+ |
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+ \item{params}{A \code{MineICAParams} object}
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+ |
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+ \item{keepVar}{The variable labels to be considered, i.e
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+ a subset of the column labels of the pheno data of icaSet |
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+ available in (\code{varLabels(icaSet)})}
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+ |
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+ \item{keepComp}{A subset of components available in
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+ \code{indComp(icaSet)}; by default, all components are
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+ used} |
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+ |
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+ \item{keepSamples}{A subset of samples, must be available
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+ in \code{sampleNames(icaSet)}; by default, all samples
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+ are used} |
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+ |
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+ \item{pathPlot}{A character specifying the path where the
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+ plots will be saved} |
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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{clusterSamplesByComp}, which consists of sample
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+ clustering applied to matrix A of argument \code{icaSet}.
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+ If missing, the clustering is performed by the function.} |
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+ |
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+ \item{funClus}{The clustering method to be used, either
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+ \code{"Mclust"} or \code{"kmeans"}. If \code{resClus} is
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+ not missing, equals \code{resClus$funClus}.}
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+ |
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+ \item{nbClus}{If \code{resClus} is missing, it provides
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+ the number of clusters to be computed by \code{funClus},
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+ default is 2} |
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+ |
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+ \item{by}{Either \code{"annot"} to plot the histograms of
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+ each variable across all components, or |
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+ \code{"component"} to plot the histograms for each
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+ component across variables. When \code{by="annot"} one
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+ pdf file is created by variable name, while when |
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+ \code{annot="component"}, one pdf file is created by
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+ component.} |
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+ |
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+ \item{typeImage}{The type of image to be created, either
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+ "pdf" (default) or "png". "png" is not recommended, |
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+ unless there are at the most 4 histograms to be plotted, |
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+ because it does not allow to deal with multiple pages of |
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+ plots.} |
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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 groups of samples |
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+ formed by the variables (i.e the sample annotations) |
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+ across all the components of an object of class |
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+ \code{\link[MineICA:IcaSet-class]{icaSet}}. For each
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+ variable level (e.g for each tumor stage) this function |
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+ plots the positions of the corresponding samples (e.g the |
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+ subset of samples having this tumor stage) within the |
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+ histogram of the global sample contributions. The plots |
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+ are saved in pdf file, one file is created per variable. |
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+ The pdf files are names 'variable.pdf' and save either in |
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+ \code{pathPlot} if specified or the current directory.
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+} |
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+\details{
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+ The plotted values are the sample contributions across |
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+ the components, i.e across the columns of |
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+ \code{A(icaSet)}.
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+ |
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+ If argument \code{resClus} is missing, the function
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+ computes the clustering of the samples on each component |
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+ (i.e on each column of \code{A(icaSet)}) using
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+ \code{funClus} and \code{nbClus}.
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+ |
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+ The association between the clusters and the considered |
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+ sample group is tested using a chi-square test. The |
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+ p-values of these tests are available in the title of |
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+ each plot. |
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+ |
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+ When \code{by="annot"} this function plots the histograms
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+ of each variable across all components, to plot the |
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+ histograms for each component across variables, please |
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+ use \code{by="component"}.
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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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+## Use icaSetCarbayo, look at the available annotations |
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+varLabels(icaSetCarbayo) |
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+ |
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+## Plot positions of samples in components according to annotations 'SEX' and 'STAGE' |
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+# plots are saved in files SEX.pdf and STAGE.pdf created in the current directory |
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+plotPosAnnotInComp(icaSet=icaSetCarbayo, keepVar=c("SEX","STAGE"), keepComp=1:2, funClus="Mclust")
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+# specifiy arg 'pathPlot' to save the pdf in another directory, but make sure it exists before |
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+# specifiy arg 'by="comp"' to create one pdf file per component |
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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{plotPosSamplesInComp}}, \code{chisq.test}
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+} |
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+ |