Package: linkcomm 1.0-14

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

Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities. Kalinka and Tomancak (2011) <doi:10.1093/bioinformatics/btr311>.

Authors:Alex T. Kalinka <[email protected]>, with contributions from Alain Guenoche

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linkcomm.pdf |linkcomm.html✨
linkcomm/json (API)
NEWS

# Install 'linkcomm' in R:

install.packages('linkcomm', repos = c('https://alextkalinka.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alextkalinka/linkcomm/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

human_pp - Sample Human Protein Interactome
karate - Social Network in a Karate Club
lesmiserables - Co-Appearance Network from Les Miserables
pp_rnapol - Sample Yeast Protein Interactome
weighted - Sample Gene Co-Expression Network

On CRAN:

clustering networks networks-biology visualization

7.39 score 7 stars 3 packages 111 scripts 436 downloads 7 mentions 33 exports 13 dependencies

Last updated 4 years agofrom:b47d5e6018. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win-x86_64	NOTE	Oct 25 2024
R-4.5-linux-x86_64	NOTE	Oct 25 2024
R-4.4-win-x86_64	OK	Oct 25 2024
R-4.4-mac-x86_64	OK	Oct 25 2024
R-4.4-mac-aarch64	OK	Oct 25 2024
R-4.3-win-x86_64	OK	Oct 25 2024
R-4.3-mac-x86_64	OK	Oct 25 2024
R-4.3-mac-aarch64	OK	Oct 25 2024

Exports:corLinkcommCentrality cutDendrogramAt edge.duplicates get.community.overlaps get.shared.nodes getAllNestedComm getClusterRelatedness getCommunityCentrality getCommunityConnectedness getCommunityMatrix getEdgesIn getLinkCommunities getNestedHierarchies getNodesIn getOCG.clusters graph.feature integer.edgelist layout.spencer.circle linkcomm2clustnsee linkcomm2cytoscape LinkDensities meta.communities newLinkCommsAt numberEdgesIn orderCommunities plotLinkCommDend plotLinkCommGraph plotLinkCommMembers plotLinkCommSumm plotLinkCommSummComm plotOCGraph read.OCG which.communities

Dependencies:cli cpp11 dynamicTreeCut glue igraph lattice lifecycle magrittr Matrix pkgconfig RColorBrewer rlang vctrs

R packages: Static PDF and HTML vignettes

Rendered fromlinkcomm.pdf.asisusingR.rsp::asison Oct 25 2024.

Last update: 2020-10-03
Started: 2020-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'linkcomm' package	linkcomm-package linkcomm
Correlation of Community Centrality with Classic Centrality	corLinkcommCentrality
Extract Meta-Communities	cutDendrogramAt
Find and Remove Edge Loops and Duplicates	edge.duplicates
Find Node Overlaps between Communities	get.community.overlaps
Get Nodes Shared by Communities	get.shared.nodes
Find Nested Communities	getAllNestedComm
Hierarchichal Clustering of Link Communities	getClusterRelatedness
Calculate Community Centrality Measures for Nodes	getCommunityCentrality
Calculate Community Connectedness or Modularity	getCommunityConnectedness
Construct a Community Membership Matrix	getCommunityMatrix
Extract Edge Indices from Communities	getEdgesIn
Extract Link Communities from a Network	getLinkCommunities
Find Nested Structures in Communities	getNestedHierarchies
Extract Nodes from Communities	getNodesIn
Generate Overlapping Cluster Generator (OCG) Communities	getOCG.clusters
Make Node or Edge Graph Features	graph.feature
Sample Human Protein Interactome	human_pp
Convert A Network to an Integer Edgelist	integer.edgelist
Social Network in a Karate Club	karate
Calculate Node Coordinates for a Spencer Circle	layout.spencer.circle
Co-Appearance Network from Les Miserables	lesmiserables
Write a Partition File for Clust&See	linkcomm2clustnsee
Write an Edge Attribute File for Cytoscape	linkcomm2cytoscape
Calculate Link Community Link Densities	LinkDensities
Produce a Set of Meta-Communities	meta.communities
User-Defined Link Communities	newLinkCommsAt
Extract Node Community Membership by Edges	numberEdgesIn
Order Link Communities According to the Dendrogram	orderCommunities
The 'linkcomm' Plotting Function	plot.linkcomm
The 'OCG' Plotting Function	plot.OCG
Plot a Coloured Dendrogram of Link Communities	plotLinkCommDend
Plot a Graph Layout of Link Communities	plotLinkCommGraph
Plot a Community Membership Matrix for Link Communities	plotLinkCommMembers
Plot a Summary of the Link Community Algorithm Output	plotLinkCommSumm
Plot a Summary of the Link Communities	plotLinkCommSummComm
Plot a Graph Layout of OCG Communities	plotOCGraph
Sample Yeast Protein Interactome	pp_rnapol
Print a Summary of a 'linkcomm' Object	print.linkcomm
Print a Summary of an 'OCG' Object	print.OCG
Read an OCG Partition File into R	read.OCG
Sample Gene Co-Expression Network	weighted
Extract Community Membership for Nodes	which.communities