topologicalAnalyzeNet: Analyze the specific state network

In mmnet: A metagenomic pipeline for systems biology

Description

Calculate Topological features of each node and linked with abundance attributes.

Usage

topologicalAnalyzeNet(g, Scatterplot = TRUE, .properties = c("betweennessCentrality", "degree", "clusteringCoefficient", "pageRank"), mode = c("all", "in", "out"), ...)

Arguments

g	a igraph network of a specific state, it can be obtained with function constructSSN
Scatterplot	logical, if show the scatterplot between topolagical features and abundance
.properties	instead of specifying the topological features in free form via the ... argument, one can specify them as a vector
mode	Character string, "out" for out-degree, "in" for in-degree and "all" for the sum of the two.
...	topological features that user want to calculate.

Details

Five most presented vertex topological feartures is provided by this function.

betweenness centrality: defined by the number of geodesics (shortest paths) going through a vertex , more details inbetweenness of package igraph

degree: the most basic structural property, represents the number of its adjacent edges.

clustringCofficient: measures the probability that the adjacent vertices of a vertex are connected

pageRank: Calculates the Google PageRank for the vertices in network

Value

a graph that add all the calculated topological features as the meta-attributes

See Also

constructSSN

Examples

##
data(anno)
data(RefDbcache)
KOAbund <- estimateAbundance(anno[[1]])

subnet  <- constructSSN(KOAbund)
topologicalAnalyzeNet(subnet)

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