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+\name{plot_heatmapsOnSel}

+\alias{plot_heatmapsOnSel}

+\title{Plot heatmap associated with each component}

+\usage{

+  plot_heatmapsOnSel(icaSet, selCutoff = 4,

+    level = c("features", "genes"), samplesOrder,

+    featuresOrder, selectionByComp, keepVar,

+    keepComp = indComp(icaSet), doSamplesDendro = TRUE,

+    doGenesDendro = TRUE,

+    heatmapCol = maPalette(low = "blue", high = "red", mid = "yellow", k = 44),

+    file = "", path = "", annot2col, ...)

+}

+\arguments{

+  \item{icaSet}{The IcaSet object}

+

+  \item{selCutoff}{A numeric threshold used to select the

+  contributing genes based on their projection values. Must

+  be either of length 1 and the same treshold is applied to

+  all components, or of length equal to the number of

+  components and one specific threshold is used for each

+  component.}

+

+  \item{samplesOrder}{A list providing the order of the

+  samples, per component, to be used in the heatmaps. If

+  missing, the contribution values of the samples are used

+  to rank the columns of the heatmaps.}

+

+  \item{featuresOrder}{A list providing the order of the

+  genes, per component, to be used in the heatmaps. If

+  missing, the projection values of the genes are used to

+  rank the rows of the heatmaps.}

+

+  \item{selectionByComp}{A list of gene projections per

+  component already restricted to the contributing genes,

+  if missing is computed by the function.}

+

+  \item{level}{A character indicating which data level is

+  used to plot the heatmaps: either \code{'features'} to

+  represent the data at the feature levels (e.g expression

+  profiles of probe sets), or \code{'genes'} to represent

+  the data at the annotated-features level (e.g gene

+  expression profiles).}

+

+  \item{keepVar}{The variable labels to be considered, i.e

+  a subset of the column labels of the pheno data of icaSet

+  available in (\code{varLabels(icaSet)})}

+

+  \item{keepComp}{A subset of components, must be included

+  in \code{indComp(icaSet)}. By default, all components are

+  used.}

+

+  \item{doSamplesDendro}{A logical indicating whether a

+  hierarchical clustering has to be performed on the data

+  matrix restricted to the contributing features/genes, and

+  whether the corresponding dendrogram has to be plotted,

+  default is TRUE.}

+

+  \item{doGenesDendro}{A logical indicating if the

+  dendrogram of features/genes has to be plotted, default

+  is FALSE.}

+

+  \item{heatmapCol}{A list of colors used to for heatmap

+  coloring (see argument \code{col} of the function

+  \code{image}).}

+

+  \item{file}{A character to add to each pdf file name.

+  This function creates one file by component named

+  "index-of-component_\code{file}.pdf" .}

+

+  \item{path}{A directory for the output pdf files, must

+  end with "/". Default is current directory.}

+

+  \item{annot2col}{A vector of colours indexed by the

+  levels of the variables of \code{icaSet} (i.e all the

+  annotation values available in \code{pData(icaSet)}). If

+  missing the colours are generated automatically using the

+  function \code{annot2Color}}

+

+  \item{...}{Additional parameters for function

+  \code{heatmap.plus}}

+}

+\value{

+  A list with one element per component, each of them being

+  a list consisting of three elements:

+  \describe{\item{x}{the matrix represented by the

+  heatmap},\item{breaks}{the breaks used for the colours of

+  the heatmap},\item{dendro}{the dendrogram}.}

+}

+\description{

+  This function plots the heatmaps representing the

+  measured values of the contributing features/genes on

+  each component. It also plots the sample annotations

+  above each heatmap using colours.

+}

+\details{

+  This function restricts the data matrix of an

+  \code{\link{IcaSet}} object to the contributing

+  genes/features, and order features/genes and samples

+  either as asked by the user or according to their values

+  in the ICA decomposition.

+

+  The heatmap is plotted using a slightly modified version

+  of the function \code{heatmap.plus} from the package of

+  the same name. By default in this function, the

+  hierarchical clustering is calculated using the function

+  \code{\link[cluster]{agnes}} with euclidean metric and

+  Ward's method.

+}

+\examples{

+\dontrun{

+## load an example of IcaSet object

+data(icaSetCarbayo)

+

+## check which variables you would like to use in the heatmap

+varLabels(icaSetCarbayo)

+keepVar <- c("STAGE","SEX")

+## Use only component 1

+keepComp <- 1

+

+## For each component, select contributing *genes* using a threshold of 2 on the absolute projection values,

+## and plot heatmaps of these contributing genes by ordering genes and samples according to their contribution values

+plot_heatmapsOnSel(icaSet = icaSetCarbayo, selCutoff = 2, level = "genes", keepVar = keepVar,

+                   keepComp=1, doSamplesDendro = TRUE, doGenesDendro = TRUE,

+                   heatmapCol = maPalette(low = "blue",high = "red", mid = "yellow", k=44),

+                   file = "heatmapWithoutDendro_zval3.pdf")

+

+## For each considered component, select contributing *features* using a threshold of 2 on the absolute projection values,

+## and plot heatmaps of these contributing genes with dendrograms

+plot_heatmapsOnSel(icaSet = icaSetCarbayo, selCutoff = 2, level = "features", keepVar = keepVar,

+                   keepComp=1, doSamplesDendro = TRUE, doGenesDendro = TRUE,

+                   heatmapCol = maPalette(low = "blue",high = "red", mid = "yellow", k=44),

+                   file = "heatmapWithDendro_zval3.pdf")

+

+

+

+}

+}

+\author{

+  Anne Biton

+}

+\seealso{

+  \code{heatmap.plus}, \code{\link{image}},

+  \code{\link{annot2Color}},

+  \code{\link{build_sortHeatmap}}

+}

+