mmnet (version 1.10.2)

showMetagenomicNet: Visualiation of metabolic network

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.

Value

• Returns NULL, invisibly.

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)

Examples

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