plotPosSamplesInComp: Histograms of sample subsets

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

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

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.

Value

NULL

Author(s)

Anne Biton

See Also

hist, IcaSet

Examples

## 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)

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.