MARVEL (version 1.4.0)

BioPathways.Plot.10x: 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)

Value

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

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.

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