plotNetworks {pairkat}R Documentation

Plot networks created by GatherNetworks function

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")


[Package pairkat version 0.99.5 Index]