inOutScatterCharts: A function to create scatter plots of the in-degree and...
In Bioconductor/ppiStats: Protein-Protein Interaction Statistical Package

Description Usage Arguments Value Author(s) Examples

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).

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

`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
`saveDir`	Directory for saving files. If none provided, `tempdir()` used by default.

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 node

The eps file contains the same information as the second pdf file.

T Chiang

data("bpExperimentNames", package = "ppiData")
graphs <- new.env(parent = emptyenv())
data(list = bpExperimentNames, package = "ppiData", envir = graphs)
graphs <- lapply(bpExperimentNames, function(x) graphs[[x]])
names(graphs) <- bpExperimentNames
inOutScatterCharts(graphs)