deps: Package dependency graphs

In lgatto/biocdownloads: Learning about Bioconductor packages

Description

This function takes a list of packages and build the their dependency graph using all packages of a repository (for example all Bioconductor software or CRAN packages). The packages of interest and all their dependencies are used to create the graph.

Usage

pkg_dep_graph(pkgs, which = c("BioCsoft", "BioCann", "BioCexp", "CRAN"))

plot_pkg_dep_graph(gr, sz = 20, fs = 50, pkgs, colour = "steelblue",
  edge_colour = "#00000040")

Arguments

pkgs	The name of the package(s) to generate and plot the dependency graph of. For plotting, it can be a list (each element of the list being highlighted using different colours) or a vector (all highlighted with the same colour) of package names to be highlighted.
which	What package repository to use to calculate dependency graphs. One of '"BioCsoft"'(default, Bioconductor software packages), '"BioCann"' (Bioconductor annotation packages), '"BioCexp"' (Bioconductor experiment packages) or '"CRAN"' (CRAN packages).
gr	A 'graphNEL' package dependency graph, as generated by 'pkg_dep_graph'.
sz	The size of the nodes. Default is 20.
fs	The font size. Default is 50.
colour	A vector of colours to be used to highlight to packages. The length of this argument must be of same length as the 'pkgs'.
edge_colour	The colour of the edges. Default in '"#00000040"'.

Details

The dependency graph is of class 'graphNL'. Plotting the graph also relies on the 'Rgraphviz' packge. None of these packages are attached to the search path, but users might need to load them if they wish to manipulate the graph and customise the visualisation.

Value

An object of class 'graphNEL' from the package 'graph'. The plotting function invisibly returns a 'Ragraph' object (from the 'Rgraphviz' package).

Author(s)

Laurent Gatto

Examples

p <- c("MSnbase", "mzR")
g <- pkg_dep_graph(pkgs = p)
g
plot_pkg_dep_graph(g, fs = 25)
plot_pkg_dep_graph(g, pkgs = p, fs = 25)
plot_pkg_dep_graph(g, pkgs = list("MSnbase", "mzR"),
                   colour = c("steelblue", "yellow"),
                   fs = 25)

lgatto/biocdownloads documentation built on May 14, 2019, 8:35 a.m.