plotPosOneAnnotLevInComp_ggplot: Plots the position of a subset of samples in the histogram of...

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

Plots the position of a subset of samples in the histogram of all samples using ggplot2.

Description

Given a sample annotation (e.g a tumor specific stage), this function plots the positions of the corresponding samples (e.g the subset of samples having this tumor stage) within the histogram of the global sample contributions. This function is called by plotPosOneAnnotInComp_ggplot and is only dedicated to the plot of the histogram using the package ggplot2.

Usage

  plotPosOneAnnotLevInComp_ggplot(annot, colAnnot, selLev,
    comp, title = NULL, colSel = "red", colAll = "grey74",
    binwidth = 0.1, geneExpr = NULL, geneRef = NULL, ...)

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
selLev	the name of the group of interest
comp	a vector of sample contributions
colSel	the colour of the histogram of the group of interest, default is "red"
colAll	the colour of the global histogram
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
title	A title for the plot
binwidth	set the width of the bins, see geom_histogram
...	other parameters given to geom_histogram

Value

An object of class ggplot2 containing the histogram

Author(s)

Anne Biton

See Also

geom_histogram

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