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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+\name{plotPosOneAnnotLevInComp_ggplot}
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+\alias{plotPosOneAnnotLevInComp_ggplot}
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+\title{Plots the position of a subset of samples in the histogram of all samples using \code{\link{ggplot2}}.}
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+\usage{
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+ plotPosOneAnnotLevInComp_ggplot(annot, colAnnot, selLev, |
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+ comp, title = NULL, colSel = "red", colAll = "grey74", |
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+ binwidth = 0.1, geneExpr = NULL, geneRef = NULL, ...) |
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+} |
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+\arguments{
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+ \item{annot}{a data.frame of dimensions 'samples x
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+ annotations' with one column corresponding to the |
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+ component to trait ("comp" column) and one column
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+ corresponding to the groups of interest ("interest"
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+ column)} |
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+ |
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+ \item{colAnnot}{the name of a column of the argument
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+ \code{annot} with the groups of interest}
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+ |
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+ \item{selLev}{the name of the group of interest}
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+ |
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+ \item{comp}{a vector of sample contributions}
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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}
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+ |
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+ \item{geneExpr}{a vector of values representative of the
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+ component, e.g the expression of the witness gene of the |
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+ component} |
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+ |
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+ \item{geneRef}{the ID of the feature/gene \code{geneExpr}
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+ corresponds to, e.g the name of the witness gene} |
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+ |
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+ \item{title}{A title for the plot}
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+ |
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+ \item{binwidth}{set the width of the bins, see
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+ \code{\link[ggplot2]{geom_histogram}}}
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+ |
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+ \item{...}{other parameters given to
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+ \code{\link[ggplot2]{geom_histogram}}}
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+} |
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+\value{
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+ An object of class ggplot2 containing the histogram |
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+} |
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+\description{
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+ Given a sample annotation (e.g a tumor specific stage), |
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+ this function plots the positions of the corresponding |
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+ samples (e.g the subset of samples having this tumor |
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+ stage) within the histogram of the global sample |
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+ contributions. This function is called by |
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+ \code{\link{plotPosOneAnnotInComp_ggplot}} and is only
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+ dedicated to the plot of the histogram using the package |
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+ \code{\link{ggplot2}}.
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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[ggplot2]{geom_histogram}}
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+} |
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+\keyword{internal}
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+ |