Description Usage Arguments Value Author(s) References See Also Examples
View source: R/linkcomm_misc.R
This function determines whether a particular community is nested within any other communities.
1 | getNestedHierarchies(x, clusid = 1, verbose = TRUE, plot = TRUE, ids = FALSE)
|
x |
An object of class |
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. |
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.
Alex T. Kalinka alex.t.kalinka@gmail.com
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.
1 2 3 4 5 6 | ## 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)
|
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.