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

Description Usage Arguments Value Author(s) See Also

View source: R/functions_comp2annot.R

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

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  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


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