showMetagenomicNet: Visualiation of metabolic network

In mmnet: A metagenomic pipeline for systems biology

Description

This function able to plot metabolic network to any R device.

Usage

showMetagenomicNet(net, mode = c("ref", "ssn", "compared"), method = c("OR","rank", "JSD"), cutoff, ...)

Arguments

net	the graph to visualization, reference metabolic network or sub-network of different samples
mode	a string, represents the property of your network, for more description in detalils
method	method used to mesure the difference abundance, more description in differentialAnalyzeNet
cutoff	numeric vector with length 2, specifies the difference thereshold, more description in details
...	additional plotting parameters. See igraph.plotting for the complete list.

Details

There are three different metabolic networks: ref - reference global network, ssn - state specific, compared - compared network between different state network.

More details on method to measure the difference abundance see differentialAnalyzeNet

cutoff: two-fold threshold commonly used in the odds-ratio test, cutoff = c(0.5, 2); enzymes with the 10% highest calculated differences and the 10% lowest differences, cutoff = c(0.1, 0.9)

Value

Returns NULL, invisibly.

Examples

# reference network
data(RefDbcache)
showMetagenomicNet(RefDbcache$network,mode="ref")

mmnet documentation built on May 31, 2017, 3:25 p.m.