plotDens2classInComp_plotOnly: Plots the densities or boxplots of the component...

Description Usage Arguments Value Author(s) See Also

View source: R/functions_comp2annot.R

Description

This internal function is called by plotDensOneAnnotInAllComp and qualVarAnalysis and is dedicated to the plot of the densities or boxplots using the package ggplot2.

Usage

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  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

Value

A

Author(s)

Anne Biton

See Also

geom_density, geom_boxplot, geom_point


Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.