Description Details Author(s) References See Also Examples

`linkcomm`

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

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")`

Alex T. Kalinka [email protected]

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

`getLinkCommunities`

, `getOCG.clusters`

, `plot.linkcomm`

, `pp_rnapol`

, `lesmiserables`

, `karate`

, `weighted`

, `igraph`

, `RColorBrewer`

, `grid`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
## 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)
``` |

```
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%
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Finishing up...2/4... 100%
Finishing up...3/4... 12%
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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%
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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%
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%
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%
Completed... 3%
sh: 1: cannot create /dev/null: Permission denied
Completed... 6%
sh: 1: cannot create /dev/null: Permission denied
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sh: 1: cannot create /dev/null: Permission denied
Completed... 13%
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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%
Completed... 25%
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Completed... 100%
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
```

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