MARVEL (version 1.4.0)

BioPathways.Plot: Plot pathway enrichment analysis results

Description

Plots user-specified enriched pathways.

Usage

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

Value

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

Arguments

MarvelObject

Marvel object. S3 object generated from BioPathways 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. gene set names.

offset

Numeric value. The -log10(p-value) on the x-axis to substract or add to increase the plot margins.

x.axis

Character string. If set to "enrichment" (default) the pathway enrichment will be displayed on the x-axis while the color intensity of the data points will reflect the -log10(adjusted p-value). If set to "pval" the -log10(adjusted p-value) will be displayed on the x-axis while the color intensity of the data points will reflect the pathway enrichment.

Details

This function plots selected gene sets returned from gene ontology analysis performed previously using BioPathways

Examples

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

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

# Plot
marvel.demo <- BioPathways.Plot(MarvelObject=marvel.demo,
                                go.terms=go.terms,
                                offset=10
                                )

# Check output
marvel.demo$DE$BioPathways$Plot