getNestedHierarchies: Find Nested Structures in Communities

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/linkcomm_misc.R

Description

This function determines whether a particular community is nested within any other communities.

Usage

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getNestedHierarchies(x, clusid = 1, verbose = TRUE, plot = TRUE, ids = FALSE)

Arguments

x

An object of class linkcomm.

clusid

An integer value indicating the community ID whose nesting structure will be tested. Defaults to 1.

verbose

Logical, whether to display a warning that a particular community is not nested in any other communities on the screen. Defaults to FALSE.

plot

Logical, whether to plot a graph layout of the nested community.

ids

Logical, whether to return only the community IDs that the community is nested in, or the node names also. Defaults to FALSE.

Value

Either a list of character vectors, each giving the nodes that the community is nested in, or an integer vector of community IDs that the community is nested in.

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.

See Also

getAllNestedComm

Examples

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

## Determine if community 1 is nested in any other communities.
getNestedHierarchies(lc, clusid = 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% 
Cluster 1 is not entirely nested in any other clusters.

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