ppiStats (version 1.36.0)

inOutScatterCharts: A function to create scatter plots of the in-degree and out-degree for each vertex of a directed graph

Description

This function takes a list of directed graph objects and plots the out-degree against the in-degree for each vertex. A binomial test is used to determine if there is a highly disproportionate in-degree or out-degree given a p-value threshold (the binomial test presumes p = 0.5).

Usage

inOutScatterCharts(dataGraphs, pThresh=0.01, pLevels=1e-4)

Arguments

dataGraphs

A named list of directed graphNELs

pThresh

The two-sided p-value threshold for the binomial testing for potentially biased nodes

pLevels

Figure out what this does

Value

For each directed data graph, this function generates 3 pdf scatter-plots and 1 eps scatter plot. The pdf files are: 1. A scatter plot of each nodes out- vs in-degree where points outside the staircase bundaries are those rejected in the binomial test. 2. A scatter plot of each nodes out- vs in-degree scaled by sqrt where points outside the conic region are those rejected in the binomial test. 3. A histogram for the distribution of p-values for each nodeThe eps file contains the same information as the second pdf file.

Examples

graphs = lapply(bpExperimentNames, function(x) get(x))
names(graphs) = bpExperimentNames
#inOutScatterCharts(graphs)