plotAnnot: Plot annotation statistics

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Plot maping statistics of an object containing mapping statistics in counts as percentages in stacked barplots.

Usage

plotAnnot(x, scope, title, group = "default", facet = NULL,
  normalise = TRUE)

## S4 method for signature 'data.frame'
plotAnnot(x, scope, title, group = "default",
  facet = NULL, normalise = TRUE)

## S4 method for signature 'DataFrame'
plotAnnot(x, scope, title, group = "default",
  facet = NULL, normalise = TRUE)

## S4 method for signature 'CAGEexp'
plotAnnot(x, scope, title, group = "default",
  facet = NULL, normalise = TRUE)

Arguments

x	An object from which can be extracted a table with columns named promoter, exon, intron, mapped, extracted, rdna, and tagdust, that will be passed to the mapStats function.
scope	The name of a “scope”, that defines which data is plotted and how it is normalised, or a function implementing that scope. See mapStatsScopes() for details on each scope.
title	The title of the plot.
group	A factor to group the samples, or the name of a colData column of a CAGEexp object, or a formula giving the names of columns to be pasted together.
facet	A factor or the name of a colData column of a CAGEexp object, to facet the samples in the sense of ggplot2's facet_wrap function.
normalise	Whether to normalise or not. Default: TRUE.

Details

Stacked barplots with error bars inspired from http://stackoverflow.com/questions/10417003/stacked-barplot-with-errorbars-using-ggplot2. See http://www.biomedcentral.com/1471-2164/14/665/figure/F1 for example.

Value

Returns invisibly a ggplot2 object of class c("gg", "ggplot").

Author(s)

Charles Plessy

See Also

mapStats() for a list of scopes.

Other CAGEr annotation functions: annotateCTSS, ranges2annot, ranges2genes, ranges2names

Other CAGEr plot functions: hanabiPlot, plotCorrelation, plotExpressionProfiles, plotInterquantileWidth, plotReverseCumulatives

Examples

p <- plotAnnot(exampleCAGEexp, 'counts', 'Here is the title')
print(p)
p + ggplot2::theme_bw()
ggplot2::theme_set(ggplot2::theme_bw()) ; p
plotAnnot(exampleCAGEexp, 'counts', 'Same, non-normalised', normalise = FALSE)
exampleCAGEexp$myGroups <- factor(c("A", "A", "B", "B", "C"))
plotAnnot(exampleCAGEexp, 'counts', group = "myGroups")
plotAnnot(exampleCAGEexp, 'counts', group = ~myGroups)
plotAnnot(exampleCAGEexp, 'counts', group = ~sampleLabels + myGroups)
plotAnnot(exampleCAGEexp, CAGEr:::msScope_counts , group = "myGroups")

CAGEr documentation built on Jan. 17, 2021, 2 a.m.