plotPosSamplesInComp: Histograms of sample subsets

Description

This function plots the positions of several groups of samples across all the components of an icaSet object.

Usage

plotPosSamplesInComp(samplesByGroup, labGroups = NULL, icaSet, keepComp = indComp(icaSet), file = NULL, breaks = 20, colAll = "grey74", colSel = "red", titlesup = "", resClus, funClus = c("Mclust", "kmeans"), ...)

Arguments

samplesByGroup

A list whose elements are vector of sample names, these sample names must be available in sampleNames(icaSet). The list should be indexed by the name of the corresponding groups.

labGroups

A vector of group names, will be used to add names to sampleByGroup if names(samplesByGroup) is NULL.

icaSet

An object of class IcaSet

keepComp

A subset of components available in indComp(icaSet), if NULL (default) all components are used

file

A pdf file

breaks

The number of breaks to be used in the histograms

colSel

The colour of the histogram of the group of interest, default is "red"

colAll

The colour of the global histogram, default is "grey74"

resClus

A list containing the outputs of function clusterSamplesByComp, which consists of results of clustering applied to matrix A of argument icaSet.

funClus

Specifies the clustering method used, either "Mclust" or "kmeans". If resClus is not missing, equals resClus$funClus.

titlesup

Additional title for the histograms

...

Additional parameters for function hist

Value

NULL

Details

For each subgroup of samples this function plots their positions within the histogram of the global sample contributions.

The values of interest are the sample contributions across the components, i.e across the columns A(icaSet).

If argument resClus is not missing, the association between the clusters and the sub-groups of samples is tested using a chi-square test. The p-values of these tests are available in the title of each plot.

Examples

Run this code

## Not run: 
# ## load an example of IcaSet
# data(icaSetCarbayo)
# 
# ## selection of sample groups according to annotations STAGE
# samplesByGroup <- lapply(split(pData(icaSetCarbayo),pData(icaSetCarbayo)[c("STAGE")]), rownames)
# # select groups including at least 2 samples
# samplesByGroup <- samplesByGroup[which(unlist(lapply(samplesByGroup,length))>1)]
# 
# ## clustering of samples according to A using Mclust imposing two Gaussian
# resClus <- clusterSamplesByComp(icaSet=icaSetCarbayo,funClus="Mclust", nbClus=2, clusterOn="A")
# 
# ## Plot positions of the groups in 5th component
# pdf(file="stageOnIC5.pdf", height = 8.267717, width = 29.7/2.54, paper = 'a4r', title="stageOnIC5")
# plotPosSamplesInComp(samplesByGroup=samplesByGroup, icaSet=icaSetCarbayo, funClus="Mclust",
#                      resClus = resClus, keepComp=5)
# dev.off()
# ## End(Not run)