Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/linkcomm_misc.R
This function extracts meta-communities from a dendrogram of community relatedness based on a user-defined place at which to cut the dendrogram.
1 2 3 |
x |
An object of class |
lc |
An object of class |
cutat |
A numerical value at which to cut the dendrogram. |
plot |
Logical, whether to plot the dendrogram and the meta-communities, defaults to TRUE. |
col |
Logical, whether to colour the meta-communites. |
pal |
A character vector describing a colour palette to be used for colouring the meta-communites in the dendrogram plot. Defaults to |
labels |
Logical, whether to put labels on the dendrogram. Defaults to FALSE. |
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 colouring the dendrogram. Defaults to TRUE. |
... |
Additional arguments to be passed to |
Extracting meta-communities allows the user to explore community relatedness and structure at higher levels.
A list of integer vectors, referring to meta-communities of link communities.
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 7 | ## Generate graph, extract link communities, and cluster communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
hc <- getClusterRelatedness(lc)
## Cut dendrogram at 1 and extract meta-communities.
cutDendrogramAt(hc, cutat = 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%
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Checking for loops and duplicate edges... 13.043%
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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%
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Checking for loops and duplicate edges... 78.261%
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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%
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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%
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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%
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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
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Plotting...
Colouring dendrogram... 1%
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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...
Extracting clusters... 0.00%
Extracting clusters... 25.00%
Extracting clusters... 50.00%
Extracting clusters... 75.00%
Extracting clusters... 100.00%
Colouring dendrogram... 6%
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Plotting...
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