plotLinkCommMembers: Plot a Community Membership Matrix for Link Communities
In linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
View source: R/linkcomm_plotting.R
Description
This function is called by plot.linkcomm to plot a community membership matrix for the link communities.
Usage
1
2
3
plotLinkCommMembers(x, nodes = head(names(x$numclusters), 10),
pal = brewer.pal(11, "Spectral"), shape = "rect", total = TRUE,
fontsize = 11, nspace = 3.5, maxclusters = 20)
Arguments
x
An object of class linkcomm.
nodes
A character vector specifying the node names that will be included in the plot. Defaults to the 10 nodes that belong to the most communities.
pal
A character vector describing a colour palette to be used for community-specific colouring. Defaults to brewer.pal(11, "Spectral").
shape
A character string specifying the shape of matrix entries. Can be one of "rect" or "circle". Defaults to "rect".
total
Logical, whether to display the number of communities each node belongs to and the number of nodes in each community. Defaults to TRUE.
fontsize
A numerical value specifying font size for the node names. Defaults to 11.
nspace
A numerical value specifying how much space to leave at the left for fitting in node names. Defaults to 3.5.
maxclusters
An integer value specifying the maximum number of communities to display. Defaults to 20.
Value
A community membership matrix plot.
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
Examples
1
2
3
4
5
6
## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Plot a community membership matrix.
plot(lc, type = "members")
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%
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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%
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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%
linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) References See Also Examples
View source: R/linkcomm_plotting.R
Description
This function is called by plot.linkcomm to plot a community membership matrix for the link communities.
Usage
1 2 3 | plotLinkCommMembers(x, nodes = head(names(x$numclusters), 10),
pal = brewer.pal(11, "Spectral"), shape = "rect", total = TRUE,
fontsize = 11, nspace = 3.5, maxclusters = 20)
|
Arguments
x |
An object of class |
nodes |
A character vector specifying the node names that will be included in the plot. Defaults to the 10 nodes that belong to the most communities. |
pal |
A character vector describing a colour palette to be used for community-specific colouring. Defaults to |
shape |
A character string specifying the shape of matrix entries. Can be one of |
total |
Logical, whether to display the number of communities each node belongs to and the number of nodes in each community. Defaults to TRUE. |
fontsize |
A numerical value specifying font size for the node names. Defaults to 11. |
nspace |
A numerical value specifying how much space to leave at the left for fitting in node names. Defaults to 3.5. |
maxclusters |
An integer value specifying the maximum number of communities to display. Defaults to 20. |
Value
A community membership matrix plot.
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
Examples
1 2 3 4 5 6 | ## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Plot a community membership matrix.
plot(lc, type = "members")
|
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%
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Finishing up...4/4... 0.00%
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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... 93%
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Colouring dendrogram... 96%
Colouring dendrogram... 97%
Colouring dendrogram... 98%
Colouring dendrogram... 100%
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