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.
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:
Linear algebra operations:
Matrix
matrixcalc
Multivariate normal simulations
mvtnorm
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.
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