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

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.
sort.y.axis.	Only applicable when custom vector of GO terms specified in the go.terms option. When set to TRUE, y-axis will be sorted as per order of custom vector of GO terms provided. Default is FALSE.

Details

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

Value

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

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

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