linkcomm-package: The 'linkcomm' package

In linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks

Description

linkcomm provides tools for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.

Details

Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type.

For a more detailed overview of how to use the package:

vignette(topic = "linkcomm", package = "linkcomm")

To run an interactive demonstration of linkcomm within R:

demo(topic = "linkcomm", package = "linkcomm")

Author(s)

Alex T. Kalinka [e-mail]

References

Ahn, Y.Y., Bagrow, J.P., and Lehmann, S. (2010). Link communities reveal multiscale complexity in networks. Nature 466, 761-764.

Becker, E., Robisson, B., Chapple, C.E., Guenoche, A. and Brun, C. (2012) Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 28, 84-90.

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.

Spencer, R. (2010). http://scaledinnovation.com/analytics/communities/comlinks.html

See Also

getLinkCommunities, getOCG.clusters, plot.linkcomm, pp_rnapol, lesmiserables, karate, weighted, igraph, RColorBrewer, grid

Examples

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

## Plot a graph layout of the link communities.
plot(lc, type = "graph")

## Use a Spencer circle layout.
plot(lc, type = "graph", layout = "spencer.circle")

## Calculate a community-based measure of node centrality.
getCommunityCentrality(lc)

## Find nested communities.
getAllNestedComm(lc)

## Uncover the relatedness between communities.
getClusterRelatedness(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% 
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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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   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% 
   Getting node community edge density...4%
   Getting node community edge density...9%
   Getting node community edge density...13%
   Getting node community edge density...18%
   Getting node community edge density...22%
   Getting node community edge density...27%
   Getting node community edge density...31%
   Getting node community edge density...36%
   Getting node community edge density...40%
   Getting node community edge density...45%
   Getting node community edge density...50%
   Getting node community edge density...54%
   Getting node community edge density...59%
   Getting node community edge density...63%
   Getting node community edge density...68%
   Getting node community edge density...72%
   Getting node community edge density...77%
   Getting node community edge density...81%
   Getting node community edge density...86%
   Getting node community edge density...90%
   Getting node community edge density...95%
   Getting node community edge density...100%
   Getting node layout...
   Constructing node pies...4%
   Constructing node pies...9%
   Constructing node pies...13%
   Constructing node pies...18%
   Constructing node pies...22%
   Constructing node pies...27%
   Constructing node pies...31%
   Constructing node pies...36%
   Constructing node pies...40%
   Constructing node pies...45%
   Constructing node pies...50%
   Constructing node pies...54%
   Constructing node pies...59%
   Constructing node pies...63%
   Constructing node pies...68%
   Constructing node pies...72%
   Constructing node pies...77%
   Constructing node pies...81%
   Constructing node pies...86%
   Constructing node pies...90%
   Constructing node pies...95%
   Constructing node pies...100%
   Ordering communities according to dendrogram...12% 
   Ordering communities according to dendrogram...25% 
   Ordering communities according to dendrogram...37% 
   Ordering communities according to dendrogram...50% 
   Ordering communities according to dendrogram...62% 
   Ordering communities according to dendrogram...75% 
   Ordering communities according to dendrogram...87% 
   Ordering communities according to dendrogram...100% 
   Calculating node co-ordinates for Spencer circle...4% 
   Calculating node co-ordinates for Spencer circle...9% 
   Calculating node co-ordinates for Spencer circle...13% 
   Calculating node co-ordinates for Spencer circle...18% 
   Calculating node co-ordinates for Spencer circle...22% 
   Calculating node co-ordinates for Spencer circle...27% 
   Calculating node co-ordinates for Spencer circle...31% 
   Calculating node co-ordinates for Spencer circle...36% 
   Calculating node co-ordinates for Spencer circle...40% 
   Calculating node co-ordinates for Spencer circle...45% 
   Calculating node co-ordinates for Spencer circle...50% 
   Calculating node co-ordinates for Spencer circle...54% 
   Calculating node co-ordinates for Spencer circle...59% 
   Calculating node co-ordinates for Spencer circle...63% 
   Calculating node co-ordinates for Spencer circle...68% 
   Calculating node co-ordinates for Spencer circle...72% 
   Calculating node co-ordinates for Spencer circle...77% 
   Calculating node co-ordinates for Spencer circle...81% 
   Calculating node co-ordinates for Spencer circle...86% 
   Calculating node co-ordinates for Spencer circle...90% 
   Calculating node co-ordinates for Spencer circle...95% 
   Calculating node co-ordinates for Spencer circle...100% 
   Getting node community edge density...4%
   Getting node community edge density...9%
   Getting node community edge density...13%
   Getting node community edge density...18%
   Getting node community edge density...22%
   Getting node community edge density...27%
   Getting node community edge density...31%
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   Getting node community edge density...40%
   Getting node community edge density...45%
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   Getting node community edge density...54%
   Getting node community edge density...59%
   Getting node community edge density...63%
   Getting node community edge density...68%
   Getting node community edge density...72%
   Getting node community edge density...77%
   Getting node community edge density...81%
   Getting node community edge density...86%
   Getting node community edge density...90%
   Getting node community edge density...95%
   Getting node community edge density...100%
   Getting node layout...
   Constructing node pies...4%
   Constructing node pies...9%
   Constructing node pies...13%
   Constructing node pies...18%
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   Constructing node pies...27%
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   Constructing node pies...77%
   Constructing node pies...81%
   Constructing node pies...86%
   Constructing node pies...90%
   Constructing node pies...95%
   Constructing node pies...100%
   Completed... 3% 
sh: 1: cannot create /dev/null: Permission denied
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       6        7       15       13       10       29        3       12 
3.000000 3.000000 2.714286 2.000000 2.000000 2.000000 2.714286 2.750000 
       5       19       17        8       16       14       21       26 
2.750000 2.142857 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 
       1       22       18        2        9       25       28       31 
1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 
      20       11       35       32       37       53 
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
   Completed... 12% 
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list()
sh: 1: cannot create /dev/null: Permission denied

   Calculating cluster similarities 1/2... 0.00%
   Calculating cluster similarities 1/2... 2.94%
   Calculating cluster similarities 1/2... 5.88%
   Calculating cluster similarities 1/2... 8.82%
   Calculating cluster similarities 1/2... 11.76%
   Calculating cluster similarities 1/2... 14.71%
   Calculating cluster similarities 1/2... 17.65%
   Calculating cluster similarities 1/2... 20.59%
   Calculating cluster similarities 1/2... 23.53%
   Calculating cluster similarities 1/2... 26.47%
   Calculating cluster similarities 1/2... 29.41%
   Calculating cluster similarities 1/2... 32.35%
   Calculating cluster similarities 1/2... 35.29%
   Calculating cluster similarities 1/2... 38.24%
   Calculating cluster similarities 1/2... 41.18%
   Calculating cluster similarities 1/2... 44.12%
   Calculating cluster similarities 1/2... 47.06%
   Calculating cluster similarities 1/2... 50.00%
   Calculating cluster similarities 1/2... 52.94%
   Calculating cluster similarities 1/2... 55.88%
   Calculating cluster similarities 1/2... 58.82%
   Calculating cluster similarities 1/2... 61.76%
   Calculating cluster similarities 1/2... 64.71%
   Calculating cluster similarities 1/2... 67.65%
   Calculating cluster similarities 1/2... 70.59%
   Calculating cluster similarities 1/2... 73.53%
   Calculating cluster similarities 1/2... 76.47%
   Calculating cluster similarities 1/2... 79.41%
   Calculating cluster similarities 1/2... 82.35%
   Calculating cluster similarities 1/2... 85.29%
   Calculating cluster similarities 1/2... 88.24%
   Calculating cluster similarities 1/2... 91.18%
   Calculating cluster similarities 1/2... 94.12%
   Calculating cluster similarities 1/2... 97.06%
   Calculating cluster similarities 2/2... 0.00%
   Calculating cluster similarities 2/2... 16.67%
   Calculating cluster similarities 2/2... 33.33%
   Calculating cluster similarities 2/2... 50.00%
   Calculating cluster similarities 2/2... 66.67%
   Calculating cluster similarities 2/2... 83.33%
   Calculating cluster similarities 2/2... 100.00%
   Hierarchical clustering...
   Plotting... 

Call:
hclust(d = distobj, method = hcmethod)

Cluster method   : ward.D 
Number of objects: 8 

linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.