Usage
plotDens2classInComp_plotOnly(annot, colAnnot, global, keepLev, comp.label = NULL, colours, legend.title = NULL, pval, test, title.add = NULL, data_ref = NULL, geneExpr = NULL, geneRef = NULL, ylab = NULL, trace_globalExpression = FALSE, trace_groupExpression = TRUE, typePlot = c("density", "boxplot"), addPoints = FALSE)
Arguments
annot
a data.frame of dimensions 'samples x
annotations' with one column corresponding to the
component to trait ("comp" column) and one column
corresponding to the groups of interest ("interest"
column)
colAnnot
the name of a column of the argument
annot with the groups of interest
global
a vector with the global distribution, e.g
the contribution values of all samples on the component
keepLev
the groups of interest, i.e the levels of
the annotation colAnnot to be considered
comp.label
the label of the component
colours
a vector of colours indexed by the names
of the groups of interest
legend.title
the title of the legend, if NULL
(default) colAnnot is used
pval
the p-value of the test, will be written in
the title
test
name of test that gave the p-value
title.add
a title to add to the automatically
generated title
data_ref
a data.frame similar to the argument
annot but restricted to a set of reference
samples
geneExpr
a vector of values representative of the
component, e.g the expression of the witness gene of the
component
geneRef
the ID of the feature/gene geneExpr
corresponds to, e.g the name of the witness gene
ylab
A label for the y-axis (character)
trace_globalExpression
if TRUE, geneExpr is
plotted below the graph as a set of points whose colour
is representative of the amount of expression, default is
FALSE
trace_groupExpression
if TRUE (default), geneExpr
is plotted below the graph, by group, as a set of points
whose colour is representative of the amount of
expression
typePlot
The type of plot, either "density" or
"boxplot"
addPoints
If TRUE, points are superimposed on the
boxplots