buildPkgDependencyIgraph: Work with package dependencies as a graph

In BiocPkgTools: Collection of simple tools for learning about Bioc Packages

Description

Package dependencies represent a directed graph (though Bioconductor dependencies are not an acyclic graph). This function simply returns an igraph graph from the package dependency data frame from a call to buildPkgDependencyDataFrame or any tidy data frame with rows of (Package, dependency) pairs. Additional columns are added as igraph edge attributes (see graph_from_data_frame).

Usage

buildPkgDependencyIgraph(pkgDepDF)

Arguments

pkgDepDF

a tidy data frame. See description for details.

Value

An igraph directed graph. See the igraph package for details of what can be done.

See Also

See buildPkgDependencyDataFrame, graph_from_data_frame, inducedSubgraphByPkgs, subgraphByDegree, igraph-es-indexing, igraph-vs-indexing

Examples

library(igraph)

pkg_dep_df = buildPkgDependencyDataFrame()

# at this point, filter or join to manipulate
# dependency data frame as you see fit.

g = buildPkgDependencyIgraph(pkg_dep_df)
g

# Look at nodes and edges
head(V(g)) # vertices
head(E(g)) # edges

# subset graph by attributes


head(sort(degree(g, mode='in'), decreasing=TRUE))
head(sort(degree(g, mode='out'), decreasing=TRUE))

BiocPkgTools documentation built on April 15, 2021, 6:01 p.m.