BioPathways.Plot.10x: Plot pathway enrichment analysis results

In wenweixiong/MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Plot pathway enrichment analysis results

Description

Plots user-specified enriched pathways.

Usage

BioPathways.Plot.10x(MarvelObject, go.terms, y.label.size = 10, offset = 0.5)

Arguments

MarvelObject	Marvel object. S3 object generated from BioPathways.10x function.
go.terms	Vector of character strings. Names of pathways to plot. Should match pathway names in column Description of MarvelObject$DE$BioPathways$Table.
y.label.size	Numeric value. Size of y-axis tick labels, i.e. pathway names.
offset	Numeric value. The value on the x-axis to substract or add to increase the plot margins.

Value

An object of class S3 containing with new slot MarvelObject$DE$BioPathways$Plot.

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

# Define top pathways to plot
go.terms <- marvel.demo.10x$DE$BioPathways$Table$Description
go.terms <- go.terms[c(1:10)]

# Plot
marvel.demo.10x <- BioPathways.Plot.10x(
                            MarvelObject=marvel.demo.10x,
                            go.terms=go.terms
                            )
# Check outpout
marvel.demo.10x$DE$BioPathways$Plot

wenweixiong/MARVEL documentation built on Aug. 5, 2024, 2:54 p.m.