Description Usage Arguments Value Author(s) References Examples
This function reads in an OCG partition file and converts it into an OCG object for use in R.
1 |
file |
A character string naming the OCG partition file. |
elfile |
A character string naming the file containing the network that the OCG partition is based upon. |
verbose |
Logical, whether to print progress to the screen. Defaults to FALSE. |
keep.out |
Logical, whether to keep the intermediate files written when reading in the OCG partition. Defaults to FALSE. |
An object of class OCG
, which is a list containing the following elements:
numbers |
An integer vector with the number of edges, nodes, and communities. |
modularity |
An integer number specifying the modularity of the network. |
Q |
A real number specifying the value of Q generated by the OCG algorithm. |
nodeclusters |
A data frame consisting of 2 columns; the first contains node names, and the second contains single community IDs for each node. All communities and their nodes are represented, but not necessarily all nodes. |
numclusters |
A named integer vector. Names are node names and integer values are the number of communities to which each node belongs. |
igraph |
An object of class |
edgelist |
A character matrix with 2 columns containing the nodes that interact with each other. |
clustsizes |
A named integer vector. Names are community IDs and integer values indicate the number of nodes that belong in each community. |
Alex T. Kalinka alex.t.kalinka@gmail.com
Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.
1 2 | ## Read an OCG partition file into R.
## Not run: oc <- read.OCG(file = "OCG_partition.txt", elfile = "network.txt")
|
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RColorBrewer
Welcome to linkcomm version 1.0-11
For a step-by-step guide to using linkcomm functions:
> vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
> demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
> citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))
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