topologicalAnalyzeNet: Analyze the specific state network

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

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.

Value

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

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

Examples

Run this code

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

subnet  <- constructSSN(KOAbund)
topologicalAnalyzeNet(subnet)