R: Tests if groups of samples are differently distributed on the...
plotDensOneAnnotInAllComp
R Documentation
Tests if groups of samples are differently distributed on the components and do the corresponding plots.
Description
Given a variable of the phenotype data (i.e vector of
sample annotations), this function tests if the groups of
samples formed by this variable are differently
distributed on the components, in terms of contribution
values. The distribution of the groups on the components
are represented using density plots. It is possible to
restrict the tests and the plots to a subset of samples
and/or components.
a variable label, i.e the label of a
column of the pheno data of icaSet available in
(varLabels(icaSet)) wich contains the groups of
interest
path
the directory where the plots will be
located
samples
a subset of sample names available in
samplenames(icaSet), if NULL (default) all samples
are used
keepComp
a subset of components available in
indComp(icaSet), if NULL (default) all components
are used
keepLev
the groups of interest, i.e the levels of
the annotation keepVar to be considered
colours
A vector of colours indexed by the
elements of keepLev, if NULL the colours are
generated automatically using annot2Color
legend.title
title of the legend
cutoff
The threshold p-value for statistical
significance
doPlot
if TRUE (default), the plots are drawn,
else if FALSE only test results are returned
onlySign
if TRUE (default), only the significant
results are plotted
resTests
a vector of p-values per component, if
NULL (default) the p-values are calculated using Wilcoxon
or Kruskal-Wallis test
Details
Wilcoxon or Kruskal-Wallis tests are applied depending on
the number of groups of interest from the considered
annotation (argument keepLev). The plots are saved
in individual files (one file per component) in arg
'path' if specified or in the current directory if not
specificied. Ech individual file is nameb
'index-of-component_colAnnot.png.' Recall that the
sample-contribution values are contained in
A(icaSet), and the sample annotations in
pData(icaSet).
One png image is created by plot and located in
path. Each image is named by
'index-of-component_keepVar.png'.
Value
Returns a data.frame of dimensions 'components x 1'
containing the results of the non-parametric tests
(Wilcoxon or Kruskal-Wallis tests) that test if the
groups of interest are differently distributed on the
components
## Not run:
## load an example of IcaSet
data(icaSetCarbayo)
## have a look at the sample annotations which are available
varLabels(icaSetCarbayo)
## with doPlot=TRUE trace the contributions of the samples according
## to their grade on the components
restests <- plotDensOneAnnotInAllComp(icaSet=icaSetCarbayo, keepVar="GRADE",
doPlot=FALSE)
## End(Not run)