plotNetworks: Plot networks created by GatherNetworks function

In Ghoshlab/pairkat: PaIRKAT

Description

Helper function for plotting networks of metabolites gathered from the KEGG pathways database using the GatherNetworks function.

Usage

plotNetworks(networks, pathway = "all", ...)

Arguments

networks	networks object obtained with GatherNetworks
pathway	Pathway to be plotted. Leaving this as 'all' will plot all pathways in 'networks'
...	Parameters to be passed to the plot (i.e. plot.igraph) function

Details

Plots the specified network(s) as an igraph

Value

a plot or list of plots generated by igraph

Examples

library(SummarizedExperiment)
data(smokers)

# Query KEGGREST API
networks <- GatherNetworks(SE = smokers, keggID = "kegg_id",
species = "hsa", minPathwaySize = 5)

# Plot all networks
plotNetworks(networks)

# Plot specific network
plotNetworks(networks,
pathway = "Glycerophospholipid metabolism",
layout = layout_with_kk,
main = "Glycerophospholipid Metabolism")

Ghoshlab/pairkat documentation built on Feb. 13, 2022, 6:15 a.m.