Anne Biton authored on 23/04/2020 18:30:14
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} |
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\arguments{
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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{keepVar}{a variable label, i.e the label of a
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column of the pheno data of icaSet available in |
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{plotDensOneAnnotInAllComp}
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+\alias{plotDensOneAnnotInAllComp}
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+\title{Tests if groups of samples are differently distributed on the components and do the corresponding plots.}
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+\usage{
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+ plotDensOneAnnotInAllComp(icaSet, keepVar, path = NULL, |
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+ samples, keepComp, keepLev = NULL, colours = NULL, |
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+ legend.title = NULL, doPlot = TRUE, cutoff = 0.05, |
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+ onlySign = TRUE, resTests) |
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+} |
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+\arguments{
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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{keepVar}{a variable label, i.e the label of a
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+ column of the pheno data of icaSet available in |
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+ (\code{varLabels(icaSet)}) wich contains the groups of
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+ interest} |
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+ |
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+ \item{path}{the directory where the plots will be
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+ located} |
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+ |
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+ \item{samples}{a subset of sample names available in
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+ \code{samplenames(icaSet)}, if NULL (default) all samples
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+ are used} |
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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{keepLev}{the groups of interest, i.e the levels of
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+ the annotation \code{keepVar} to be considered}
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+ |
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+ \item{colours}{A vector of colours indexed by the
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+ elements of \code{keepLev}, if NULL the colours are
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+ generated automatically using annot2Color} |
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+ |
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+ \item{legend.title}{title of the legend}
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+ |
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+ \item{cutoff}{The threshold p-value for statistical
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+ significance} |
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+ |
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+ \item{doPlot}{if TRUE (default), the plots are drawn,
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+ else if FALSE only test results are returned} |
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+ |
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+ \item{onlySign}{if TRUE (default), only the significant
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+ results are plotted} |
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+ |
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+ \item{resTests}{a vector of p-values per component, if
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+ NULL (default) the p-values are calculated using Wilcoxon |
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+ or Kruskal-Wallis test} |
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+} |
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+\value{
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+ Returns a data.frame of dimensions 'components x 1' |
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+ containing the results of the non-parametric tests |
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+ (Wilcoxon or Kruskal-Wallis tests) that test if the |
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+ groups of interest are differently distributed on the |
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+ components |
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+} |
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+\description{
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+ Given a variable of the phenotype data (i.e vector of |
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+ sample annotations), this function tests if the groups of |
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+ samples formed by this variable are differently |
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+ distributed on the components, in terms of contribution |
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+ values. The distribution of the groups on the components |
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+ are represented using density plots. It is possible to |
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+ restrict the tests and the plots to a subset of samples |
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+ and/or components. |
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+} |
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+\details{
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+ Wilcoxon or Kruskal-Wallis tests are applied depending on |
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+ the number of groups of interest from the considered |
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+ annotation (argument \code{keepLev}). The plots are saved
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+ in individual files (one file per component) in arg |
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+ 'path' if specified or in the current directory if not |
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+ specificied. Ech individual file is nameb |
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+ 'index-of-component_colAnnot.png.' Recall that the |
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+ sample-contribution values are contained in |
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+ \code{A(icaSet)}, and the sample annotations in
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+ \code{pData(icaSet)}.
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+ |
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+ One png image is created by plot and located in |
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+ \code{path}. Each image is named by
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+ 'index-of-component_keepVar.png'. |
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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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+## have a look at the sample annotations which are available |
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+varLabels(icaSetCarbayo) |
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+ |
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+## with doPlot=TRUE trace the contributions of the samples according |
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+## to their grade on the components |
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+restests <- plotDensOneAnnotInAllComp(icaSet=icaSetCarbayo, keepVar="GRADE", |
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+ doPlot=FALSE) |
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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{wilcoxOrKruskalOnA}},
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+ code{\link{writeHtmlResTestsByAnnot}},
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+ code{\link{wilcox.test}}, code{\link{kruskal.test}}
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+} |
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+\keyword{internal}
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+ |