README.md

In TomKellyGenetics/igraph.extensions: Easily install and load the igraph package and extensions

igraph.extensions

metapackage: Easily install and load the igraph package and extensions

The igraph.extensions are a set of packages that add additional functionality to the igraph R package. This metapackage makes it convenient to install and load the set of packages and their dependencies in a single command.

See the relevant documentation and vignettes for the extensions or the igraph package.

Installation

You can install these packages from github with:

# install.packages("devtools")
devtools::install_github("TomKellyGenetics/igraph.extensions")

This will install the set packages of that you are often used together:

• plot.igraph, for custom plotting of directed graphs with multiple edge states (activator/inhibitor arrows).
• info.centrality, for computing information centrality of vertices or networks and the network efficiency metric required to do so.
• pathway.structure.permutation, for testing the relationships between node states or annotations (e.g., gene function or significance).
• graphsim, for simulating continous multi-variate normal data (e.g., gene expression) from a graph network (e.g., gene regulation pathhway), includes options for derving sigma matrix from various derived adjacency or distance matrices and negative correlations/covariances for inhibitor edge states.

This also installs dependancies for these packages including:

• Working with graph objects:

  • igraph

• Linear algebra operations:

  • Matrix
  • matrixcalc

• Multivariate normal simulations

  • mvtnorm

Usage

These packages can be loaded them explicitly with library().

library("igraph")
library("plot.igraph")
library("graphsim")

However, more conveniently, all required packages can be loaded together with library("igraph.extensions") with a summary of the packages you have loaded:

library("igraph.extensions")
#> Attaching package: ‘igraph’
#> 
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> 
#> The following object is masked from ‘package:base’:
#> 
#>     union
#> 
#> Loading igraph
#> Loading igraph.extensions: plot.igraph
#> Loading igraph.extensions: info.centrality
#> Loading igraph.extensions: pathway.structure.permutation
#> Loading igraph.extensions: graphsim

Note that only particular functions are imported from matrixcalc to avoid conflicts.

TomKellyGenetics/igraph.extensions documentation built on May 9, 2019, 4:53 p.m.