getNodesIn: Extract Nodes from Communities
In linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Description
Usage
Arguments
Value
Author(s)
References
Examples
View source: R/linkcomm_misc.R
Description
This function returns node names that belong to sets of communities.
Usage
1
getNodesIn(x, clusterids = 1, type = "names")
Arguments
x
An object of class linkcomm or OCG.
clusterids
An integer vector of community IDs. Defaults to community 1.
type
A character string specifying how nodes are returned. Can be one of "names" or "indices".
Value
A character vector of node names (if type is "names") or a numerical vector of node indices (if type is "indices").
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
1
2
3
4
5
6
## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Get nodes from community 1.
getNodesIn(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%
Finishing up...1/4... 87%
Finishing up...1/4... 100%
Finishing up...2/4... 12%
Finishing up...2/4... 25%
Finishing up...2/4... 37%
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%
Finishing up...3/4... 37%
Finishing up...3/4... 50%
Finishing up...3/4... 62%
Finishing up...3/4... 75%
Finishing up...3/4... 87%
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%
Colouring dendrogram... 6%
Colouring dendrogram... 7%
Colouring dendrogram... 8%
Colouring dendrogram... 9%
Colouring dendrogram... 11%
Colouring dendrogram... 12%
Colouring dendrogram... 13%
Colouring dendrogram... 14%
Colouring dendrogram... 16%
Colouring dendrogram... 17%
Colouring dendrogram... 18%
Colouring dendrogram... 19%
Colouring dendrogram... 20%
Colouring dendrogram... 22%
Colouring dendrogram... 23%
Colouring dendrogram... 24%
Colouring dendrogram... 25%
Colouring dendrogram... 27%
Colouring dendrogram... 28%
Colouring dendrogram... 29%
Colouring dendrogram... 30%
Colouring dendrogram... 32%
Colouring dendrogram... 33%
Colouring dendrogram... 34%
Colouring dendrogram... 35%
Colouring dendrogram... 37%
Colouring dendrogram... 38%
Colouring dendrogram... 39%
Colouring dendrogram... 40%
Colouring dendrogram... 41%
Colouring dendrogram... 43%
Colouring dendrogram... 44%
Colouring dendrogram... 45%
Colouring dendrogram... 46%
Colouring dendrogram... 48%
Colouring dendrogram... 49%
Colouring dendrogram... 50%
Colouring dendrogram... 51%
Colouring dendrogram... 53%
Colouring dendrogram... 54%
Colouring dendrogram... 55%
Colouring dendrogram... 56%
Colouring dendrogram... 58%
Colouring dendrogram... 59%
Colouring dendrogram... 60%
Colouring dendrogram... 61%
Colouring dendrogram... 62%
Colouring dendrogram... 64%
Colouring dendrogram... 65%
Colouring dendrogram... 66%
Colouring dendrogram... 67%
Colouring dendrogram... 69%
Colouring dendrogram... 70%
Colouring dendrogram... 71%
Colouring dendrogram... 72%
Colouring dendrogram... 74%
Colouring dendrogram... 75%
Colouring dendrogram... 76%
Colouring dendrogram... 77%
Colouring dendrogram... 79%
Colouring dendrogram... 80%
Colouring dendrogram... 81%
Colouring dendrogram... 82%
Colouring dendrogram... 83%
Colouring dendrogram... 85%
Colouring dendrogram... 86%
Colouring dendrogram... 87%
Colouring dendrogram... 88%
Colouring dendrogram... 90%
Colouring dendrogram... 91%
Colouring dendrogram... 92%
Colouring dendrogram... 93%
Colouring dendrogram... 95%
Colouring dendrogram... 96%
Colouring dendrogram... 97%
Colouring dendrogram... 98%
Colouring dendrogram... 100%
[1] "17" "15" "8"
linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) References Examples
View source: R/linkcomm_misc.R
Description
This function returns node names that belong to sets of communities.
Usage
1 | getNodesIn(x, clusterids = 1, type = "names")
|
Arguments
x |
An object of class |
clusterids |
An integer vector of community IDs. Defaults to community 1. |
type |
A character string specifying how nodes are returned. Can be one of |
Value
A character vector of node names (if type is "names") or a numerical vector of node indices (if type is "indices").
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
1 2 3 4 5 6 | ## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Get nodes from community 1.
getNodesIn(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%
Finishing up...1/4... 87%
Finishing up...1/4... 100%
Finishing up...2/4... 12%
Finishing up...2/4... 25%
Finishing up...2/4... 37%
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%
Finishing up...3/4... 37%
Finishing up...3/4... 50%
Finishing up...3/4... 62%
Finishing up...3/4... 75%
Finishing up...3/4... 87%
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%
Colouring dendrogram... 6%
Colouring dendrogram... 7%
Colouring dendrogram... 8%
Colouring dendrogram... 9%
Colouring dendrogram... 11%
Colouring dendrogram... 12%
Colouring dendrogram... 13%
Colouring dendrogram... 14%
Colouring dendrogram... 16%
Colouring dendrogram... 17%
Colouring dendrogram... 18%
Colouring dendrogram... 19%
Colouring dendrogram... 20%
Colouring dendrogram... 22%
Colouring dendrogram... 23%
Colouring dendrogram... 24%
Colouring dendrogram... 25%
Colouring dendrogram... 27%
Colouring dendrogram... 28%
Colouring dendrogram... 29%
Colouring dendrogram... 30%
Colouring dendrogram... 32%
Colouring dendrogram... 33%
Colouring dendrogram... 34%
Colouring dendrogram... 35%
Colouring dendrogram... 37%
Colouring dendrogram... 38%
Colouring dendrogram... 39%
Colouring dendrogram... 40%
Colouring dendrogram... 41%
Colouring dendrogram... 43%
Colouring dendrogram... 44%
Colouring dendrogram... 45%
Colouring dendrogram... 46%
Colouring dendrogram... 48%
Colouring dendrogram... 49%
Colouring dendrogram... 50%
Colouring dendrogram... 51%
Colouring dendrogram... 53%
Colouring dendrogram... 54%
Colouring dendrogram... 55%
Colouring dendrogram... 56%
Colouring dendrogram... 58%
Colouring dendrogram... 59%
Colouring dendrogram... 60%
Colouring dendrogram... 61%
Colouring dendrogram... 62%
Colouring dendrogram... 64%
Colouring dendrogram... 65%
Colouring dendrogram... 66%
Colouring dendrogram... 67%
Colouring dendrogram... 69%
Colouring dendrogram... 70%
Colouring dendrogram... 71%
Colouring dendrogram... 72%
Colouring dendrogram... 74%
Colouring dendrogram... 75%
Colouring dendrogram... 76%
Colouring dendrogram... 77%
Colouring dendrogram... 79%
Colouring dendrogram... 80%
Colouring dendrogram... 81%
Colouring dendrogram... 82%
Colouring dendrogram... 83%
Colouring dendrogram... 85%
Colouring dendrogram... 86%
Colouring dendrogram... 87%
Colouring dendrogram... 88%
Colouring dendrogram... 90%
Colouring dendrogram... 91%
Colouring dendrogram... 92%
Colouring dendrogram... 93%
Colouring dendrogram... 95%
Colouring dendrogram... 96%
Colouring dendrogram... 97%
Colouring dendrogram... 98%
Colouring dendrogram... 100%
[1] "17" "15" "8"
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