plotExpressionProfiles: Plot CAGE expression profiles

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

Plot CAGE expression profiles

Description

Beanplot of distribution of normalized expression across CAGE experiments for individual expression classes, colored and labeled according to the information set when expression clustering was performed.

Usage

plotExpressionProfiles(object, what)

## S4 method for signature 'CAGEexp'
plotExpressionProfiles(object, what = c("CTSS", "consensusClusters"))

Arguments

object	A CAGEr object.
what	CTSS or consensusClusters.

Details

The beanplots are shown in one labeled box per expression class. Each beanplot represents one CAGE experiment. The vertical axis represents scaled normalized expression. The color of each class is determined by the labels returned by expression clustering.

Author(s)

Vanja Haberle

Charles Plessy

See Also

Other CAGEr plot functions: hanabiPlot(), plotAnnot(), plotCorrelation(), plotInterquantileWidth(), plotReverseCumulatives()

Other CAGEr expression clustering functions: expressionClasses(), getExpressionProfiles()

Examples

plotExpressionProfiles(exampleCAGEexp, what = "CTSS")
exampleCAGEexp |> plotExpressionProfiles("consensusClusters")

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.