getClusterRelatedness: Hierarchichal Clustering of Link Communities

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

Description

This function hierarchically clusters the link communities themselves and returns an object of class hclust.

Usage

getClusterRelatedness(x, clusterids = 1:x$numbers[3], hcmethod = "ward.D", 
        cluster = TRUE, plot = TRUE, cutat = NULL, col = TRUE, 
        pal = brewer.pal(11, "Spectral"), labels = FALSE, plotcut = TRUE, 
        right = TRUE, verbose = TRUE, ...)

Arguments

x	An object of class linkcomm.
clusterids	An integer vector of community IDs. Defaults to all communities.
hcmethod	A character string naming the hierarchical clustering method to use. Can be one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", or "centroid". Defaults to "ward.D".
cluster	Logical, whether to cluster the communities. If FALSE, the function returns the upper triangular dissimilarity matrix as a vector. Defaults to TRUE.
plot	Logical, whether to plot the cluster dendrogram.
cutat	A numerical value at which to cut the dendrogram. If NULL, the dendrogram is not cut and meta-communities are not returned. Defaults to NULL.
col	Logical, whether to colour the dendrogram. Defaults to TRUE.
pal	A character vector describing a colour palette to be used for colouring the meta-communites in the dendrogram plot. Defaults to brewer.pal(11, "Spectral").
labels	Logical, whether to add labels to the dendrogram plot.
plotcut	Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE.
right	Logical, whether to orient the dendrogram to the right. Defaults to TRUE.
verbose	Logical, whether to display the progress of the calculation on the screen. Defaults to TRUE.
...	Additional arguments to be passed to plot.

Details

Extracting meta-communities allows the user to explore community relatedness and structure at higher levels. Community relatedness is calculated using the Jaccard coefficient and the number of nodes that community i and j share:

S(i,j)=|intersect(i,j)|/|union(i,j)|

Value

Either a numerical vector (the upper triangular dissimilarity matrix - if cluster = FALSE), a list of integer vectors (the meta-communities - if cutat is not NULL), or an object of class hclust (if cluster is TRUE and cutat is NULL).

Author(s)

Alex T. Kalinka [e-mail]

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.

See Also

meta.communities, cutDendrogramAt, hclust

Examples

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

## Cluster the link communities.
getClusterRelatedness(lc)

## Cluster the link communities, cut the dendrogram, and return the meta-communities.
getClusterRelatedness(lc, cutat = 1)

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% 
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 

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...

   Extracting clusters... 0.00%
   Extracting clusters... 25.00%
   Extracting clusters... 50.00%
   Extracting clusters... 75.00%
   Extracting clusters... 100.00%
   Colouring dendrogram... 6% 
   Colouring dendrogram... 13% 
   Colouring dendrogram... 20% 
   Colouring dendrogram... 26% 
   Colouring dendrogram... 33% 
   Colouring dendrogram... 40% 
   Colouring dendrogram... 46% 
   Colouring dendrogram... 53% 
   Colouring dendrogram... 60% 
   Colouring dendrogram... 66% 
   Colouring dendrogram... 73% 
   Colouring dendrogram... 80% 
   Colouring dendrogram... 86% 
   Colouring dendrogram... 93% 
   Colouring dendrogram... 100% 
   Plotting... 
[[1]]
[1] 2 5

[[2]]
[1] 3 7 8

[[3]]
[1] 1 4 6

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