get.community.overlaps: Find Node Overlaps between Communities

Description Usage Arguments Value Author(s) References Examples

View source: R/linkcomm_misc.R

Description

This function returns lists of communities that share at least one node with each other.

Usage

1

Arguments

x

An object of class linkcomm or OCG.

Value

A list of length equal to the number of communities. Each element contains an integer vector giving the community IDs for communities sharing at least one node with each community. NAs indicate that a community shares no nodes with any other communities.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

References

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.

Examples

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## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)

## Get list of overlapping communities.
ov <- get.community.overlaps(lc)

Example output

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"))


   Checking for loops and duplicate edges... 0.000%
   Checking for loops and duplicate edges... 2.174%
   Checking for loops and duplicate edges... 4.348%
   Checking for loops and duplicate edges... 6.522%
   Checking for loops and duplicate edges... 8.696%
   Checking for loops and duplicate edges... 10.870%
   Checking for loops and duplicate edges... 13.043%
   Checking for loops and duplicate edges... 15.217%
   Checking for loops and duplicate edges... 17.391%
   Checking for loops and duplicate edges... 19.565%
   Checking for loops and duplicate edges... 21.739%
   Checking for loops and duplicate edges... 23.913%
   Checking for loops and duplicate edges... 26.087%
   Checking for loops and duplicate edges... 28.261%
   Checking for loops and duplicate edges... 30.435%
   Checking for loops and duplicate edges... 32.609%
   Checking for loops and duplicate edges... 34.783%
   Checking for loops and duplicate edges... 36.957%
   Checking for loops and duplicate edges... 39.130%
   Checking for loops and duplicate edges... 41.304%
   Checking for loops and duplicate edges... 43.478%
   Checking for loops and duplicate edges... 45.652%
   Checking for loops and duplicate edges... 47.826%
   Checking for loops and duplicate edges... 50.000%
   Checking for loops and duplicate edges... 52.174%
   Checking for loops and duplicate edges... 54.348%
   Checking for loops and duplicate edges... 56.522%
   Checking for loops and duplicate edges... 58.696%
   Checking for loops and duplicate edges... 60.870%
   Checking for loops and duplicate edges... 63.043%
   Checking for loops and duplicate edges... 65.217%
   Checking for loops and duplicate edges... 67.391%
   Checking for loops and duplicate edges... 69.565%
   Checking for loops and duplicate edges... 71.739%
   Checking for loops and duplicate edges... 73.913%
   Checking for loops and duplicate edges... 76.087%
   Checking for loops and duplicate edges... 78.261%
   Checking for loops and duplicate edges... 80.435%
   Checking for loops and duplicate edges... 82.609%
   Checking for loops and duplicate edges... 84.783%
   Checking for loops and duplicate edges... 86.957%
   Checking for loops and duplicate edges... 89.130%
   Checking for loops and duplicate edges... 91.304%
   Checking for loops and duplicate edges... 93.478%
   Checking for loops and duplicate edges... 95.652%
   Checking for loops and duplicate edges... 97.826%
   Checking for loops and duplicate edges... 100.000%
   Found and removed 4 loop(s)
   Found and removed 2 duplicate edge(s)

   Calculating edge similarities for 41 edges... 0.00%
   Calculating edge similarities for 41 edges... 2.56%
   Calculating edge similarities for 41 edges... 5.13%
   Calculating edge similarities for 41 edges... 7.69%
   Calculating edge similarities for 41 edges... 10.26%
   Calculating edge similarities for 41 edges... 12.82%
   Calculating edge similarities for 41 edges... 15.38%
   Calculating edge similarities for 41 edges... 17.95%
   Calculating edge similarities for 41 edges... 20.51%
   Calculating edge similarities for 41 edges... 23.08%
   Calculating edge similarities for 41 edges... 25.64%
   Calculating edge similarities for 41 edges... 28.21%
   Calculating edge similarities for 41 edges... 30.77%
   Calculating edge similarities for 41 edges... 33.33%
   Calculating edge similarities for 41 edges... 35.90%
   Calculating edge similarities for 41 edges... 38.46%
   Calculating edge similarities for 41 edges... 41.03%
   Calculating edge similarities for 41 edges... 43.59%
   Calculating edge similarities for 41 edges... 46.15%
   Calculating edge similarities for 41 edges... 48.72%
   Calculating edge similarities for 41 edges... 51.28%
   Calculating edge similarities for 41 edges... 53.85%
   Calculating edge similarities for 41 edges... 56.41%
   Calculating edge similarities for 41 edges... 58.97%
   Calculating edge similarities for 41 edges... 61.54%
   Calculating edge similarities for 41 edges... 64.10%
   Calculating edge similarities for 41 edges... 66.67%
   Calculating edge similarities for 41 edges... 69.23%
   Calculating edge similarities for 41 edges... 71.79%
   Calculating edge similarities for 41 edges... 74.36%
   Calculating edge similarities for 41 edges... 76.92%
   Calculating edge similarities for 41 edges... 79.49%
   Calculating edge similarities for 41 edges... 82.05%
   Calculating edge similarities for 41 edges... 84.62%
   Calculating edge similarities for 41 edges... 87.18%
   Calculating edge similarities for 41 edges... 89.74%
   Calculating edge similarities for 41 edges... 92.31%
   Calculating edge similarities for 41 edges... 94.87%
   Calculating edge similarities for 41 edges... 97.44%
   Calculating edge similarities for 41 edges... 100.00%
   Hierarchical clustering of edges...

   Calculating link densities... 0.00%
   Calculating link densities... 2.56%
   Calculating link densities... 5.13%
   Calculating link densities... 7.69%
   Calculating link densities... 10.26%
   Calculating link densities... 12.82%
   Calculating link densities... 15.38%
   Calculating link densities... 17.95%
   Calculating link densities... 20.51%
   Calculating link densities... 23.08%
   Calculating link densities... 25.64%
   Calculating link densities... 28.21%
   Calculating link densities... 30.77%
   Calculating link densities... 33.33%
   Calculating link densities... 35.90%
   Calculating link densities... 38.46%
   Calculating link densities... 41.03%
   Calculating link densities... 43.59%
   Calculating link densities... 46.15%
   Calculating link densities... 48.72%
   Calculating link densities... 51.28%
   Calculating link densities... 53.85%
   Calculating link densities... 56.41%
   Calculating link densities... 58.97%
   Calculating link densities... 61.54%
   Calculating link densities... 64.10%
   Calculating link densities... 66.67%
   Calculating link densities... 69.23%
   Calculating link densities... 71.79%
   Calculating link densities... 74.36%
   Calculating link densities... 76.92%
   Calculating link densities... 79.49%
   Calculating link densities... 82.05%
   Calculating link densities... 84.62%
   Calculating link densities... 87.18%
   Calculating link densities... 89.74%
   Calculating link densities... 92.31%
   Calculating link densities... 94.87%
   Calculating link densities... 97.44%
   Calculating link densities... 100.00%
   Maximum partition density =  0.2601626 
   Finishing up...1/4... 12% 
   Finishing up...1/4... 25% 
   Finishing up...1/4... 37% 
   Finishing up...1/4... 50% 
   Finishing up...1/4... 62% 
   Finishing up...1/4... 75% 
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   Finishing up...1/4... 100% 
   Finishing up...2/4... 12% 
   Finishing up...2/4... 25% 
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   Finishing up...2/4... 50% 
   Finishing up...2/4... 62% 
   Finishing up...2/4... 75% 
   Finishing up...2/4... 87% 
   Finishing up...2/4... 100% 
   Finishing up...3/4... 12% 
   Finishing up...3/4... 25% 
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   Finishing up...3/4... 62% 
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   Finishing up...3/4... 100% 

   Finishing up...4/4... 0.00%
   Finishing up...4/4... 4.76%
   Finishing up...4/4... 9.52%
   Finishing up...4/4... 14.29%
   Finishing up...4/4... 19.05%
   Finishing up...4/4... 23.81%
   Finishing up...4/4... 28.57%
   Finishing up...4/4... 33.33%
   Finishing up...4/4... 38.10%
   Finishing up...4/4... 42.86%
   Finishing up...4/4... 47.62%
   Finishing up...4/4... 52.38%
   Finishing up...4/4... 57.14%
   Finishing up...4/4... 61.90%
   Finishing up...4/4... 66.67%
   Finishing up...4/4... 71.43%
   Finishing up...4/4... 76.19%
   Finishing up...4/4... 80.95%
   Finishing up...4/4... 85.71%
   Finishing up...4/4... 90.48%
   Finishing up...4/4... 95.24%
   Finishing up...4/4... 100.00%
   Plotting...
   Colouring dendrogram... 1% 
   Colouring dendrogram... 2% 
   Colouring dendrogram... 3% 
   Colouring dendrogram... 4% 
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linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.