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resolve Windows warnings occuring in the build 'file link 'MineICAParams-class' in package 'MineICA' does not exist and so has been treated as a topic'

Anne Biton authored on 23/04/2020 18:30:14
Showing 1 changed files
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@@ -19,7 +19,7 @@
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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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Browse code

Adds MineICA, SomatiCA and lpNet to the repos.

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
Showing 1 changed files
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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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+