R: Tests if groups of samples are differently distributed on the...
plotPosOneAnnotInComp_ggplot
R Documentation
Tests if groups of samples are differently distributed on the components and do the corresponding plots.
Description
Given a variable of the phenoData, this function tests if
the groups of samples formed by this variable are
differently distributed, in terms of contribution value
(i.e of values in matrix A(icaSet)), on the
components. 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.
An object of the class MineICAParams
containing the parameters of the analysis
colAnnot
a variable label, i.e one of the
variables available in (varLabels(icaSet))
containing the groups of interest
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 variable colAnnot to be considered
colAll
The colour of the global histogram, default
is "grey74"
file
the file where the histograms will be
plotted
addExpr
if TRUE (default) the expression profiles
of the witness genes of each component are added below
the plot
binwidth
binwidth of the histogram (default is
0.1)
...
other parameters for geom_histogram function
from ggplot2 package
Details
Wilcoxon or Kruskal-Wallis tests are applied depending on
the number of groups of interest from the considered
annotation (argument keepLev). One png image is
created by plot and located in path. Each image is
named by component-of-component_colAnnot.png.
providing 
.