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.

AuthorAlex T. Kalinka <alex.t.kalinka@gmail.com>, with contributions from Alain Guenoche
Date of publication2014-08-13 19:00:50
MaintainerAlex T. Kalinka <alex.t.kalinka@gmail.com>
LicenseGPL (>= 2)
Version1.0-11

View on CRAN

Man pages

corLinkcommCentrality: Correlation of Community Centrality with Classic Centrality

cutDendrogramAt: Extract Meta-Communities

edge.duplicates: Find and Remove Edge Loops and Duplicates

getAllNestedComm: Find Nested Communities

getClusterRelatedness: Hierarchichal Clustering of Link Communities

getCommunityCentrality: Calculate Community Centrality Measures for Nodes

getCommunityConnectedness: Calculate Community Connectedness or Modularity

getCommunityMatrix: Construct a Community Membership Matrix

get.community.overlaps: Find Node Overlaps between Communities

getEdgesIn: Extract Edge Indices from Communities

getLinkCommunities: Extract Link Communities from a Network

getNestedHierarchies: Find Nested Structures in Communities

getNodesIn: Extract Nodes from Communities

getOCG.clusters: Generate Overlapping Cluster Generator (OCG) Communities

get.shared.nodes: Get Nodes Shared by Communities

graph.feature: Make Node or Edge Graph Features

human_pp: Sample Human Protein Interactome

integer.edgelist: Convert A Network to an Integer Edgelist

karate: Social Network in a Karate Club

layout.spencer.circle: Calculate Node Coordinates for a Spencer Circle

lesmiserables: Co-Appearance Network from Les Miserables

linkcomm2clustnsee: Write a Partition File for Clust&See

linkcomm2cytoscape: Write an Edge Attribute File for Cytoscape

linkcomm-package: The 'linkcomm' package

LinkDensities: Calculate Link Community Link Densities

meta.communities: Produce a Set of Meta-Communities

newLinkCommsAt: User-Defined Link Communities

numberEdgesIn: Extract Node Community Membership by Edges

orderCommunities: Order Link Communities According to the Dendrogram

plot.linkcomm: The 'linkcomm' Plotting Function

plotLinkCommDend: Plot a Coloured Dendrogram of Link Communities

plotLinkCommGraph: Plot a Graph Layout of Link Communities

plotLinkCommMembers: Plot a Community Membership Matrix for Link Communities

plotLinkCommSumm: Plot a Summary of the Link Community Algorithm Output

plotLinkCommSummComm: Plot a Summary of the Link Communities

plot.OCG: The 'OCG' Plotting Function

plotOCGraph: Plot a Graph Layout of OCG Communities

pp_rnapol: Sample Yeast Protein Interactome

print.linkcomm: Print a Summary of a 'linkcomm' Object

print.OCG: Print a Summary of an 'OCG' Object

read.OCG: Read an OCG Partition File into R

weighted: Sample Gene Co-Expression Network

which.communities: Extract Community Membership for Nodes

Functions

corLinkcommCentrality Man page
cutDendrogramAt Man page
edge.duplicates Man page
getAllNestedComm Man page
getClusterRelatedness Man page
getCommunityCentrality Man page
getCommunityConnectedness Man page
getCommunityMatrix Man page
get.community.overlaps Man page
getEdgesIn Man page
getLinkCommunities Man page
getNestedHierarchies Man page
getNodesIn Man page
getOCG.clusters Man page
get.shared.nodes Man page
graph.feature Man page
human_pp Man page
integer.edgelist Man page
karate Man page
layout.spencer.circle Man page
lesmiserables Man page
linkcomm Man page
linkcomm2clustnsee Man page
linkcomm2cytoscape Man page
linkcomm-package Man page
LinkDensities Man page
meta.communities Man page
newLinkCommsAt Man page
numberEdgesIn Man page
orderCommunities Man page
plot.linkcomm Man page
plotLinkCommDend Man page
plotLinkCommGraph Man page
plotLinkCommMembers Man page
plotLinkCommSumm Man page
plotLinkCommSummComm Man page
plot.OCG Man page
plotOCGraph Man page
pp_rnapol Man page
print.linkcomm Man page
print.OCG Man page
read.OCG Man page
weighted Man page
which.communities Man page

Files

linkcomm
linkcomm/inst
linkcomm/inst/CITATION
linkcomm/inst/doc
linkcomm/inst/doc/linkcomm.Rnw
linkcomm/inst/doc/linkcomm.R
linkcomm/inst/doc/linkcomm.pdf
linkcomm/src
linkcomm/src/linkcomm_functions.cpp
linkcomm/src/linkcommhclust_order.cpp
linkcomm/src/linkcomm_linkdensities.cpp
linkcomm/src/linkcomm_hclust.cpp
linkcomm/src/OCG_algorithm.c
linkcomm/src/edge_duplicates.cpp
linkcomm/src/read_OCG.cpp
linkcomm/src/linkcomm_edgesims_all.cpp
linkcomm/src/linkcomm_edgesims.cpp
linkcomm/NAMESPACE
linkcomm/demo
linkcomm/demo/linkcomm.R
linkcomm/demo/00Index
linkcomm/NEWS
linkcomm/data
linkcomm/data/networks.rda
linkcomm/R
linkcomm/R/linkcomm_plotting.R linkcomm/R/linkcomm_misc.R linkcomm/R/linkcomm_main.R linkcomm/R/OCG_main.R
linkcomm/vignettes
linkcomm/vignettes/nodepie_linkcomm.pdf
linkcomm/vignettes/graph_layout_examples.pdf
linkcomm/vignettes/custom_graphs.pdf
linkcomm/vignettes/linkcomm.Rnw
linkcomm/vignettes/networks.rda
linkcomm/vignettes/cluster_relatedness.pdf
linkcomm/vignettes/ocg_lesmis.pdf
linkcomm/vignettes/fig1_vignette.pdf
linkcomm/MD5
linkcomm/build
linkcomm/build/vignette.rds
linkcomm/DESCRIPTION
linkcomm/man
linkcomm/man/getOCG.clusters.Rd linkcomm/man/edge.duplicates.Rd linkcomm/man/getLinkCommunities.Rd linkcomm/man/getNodesIn.Rd linkcomm/man/linkcomm2cytoscape.Rd linkcomm/man/which.communities.Rd linkcomm/man/layout.spencer.circle.Rd linkcomm/man/getCommunityMatrix.Rd linkcomm/man/linkcomm-package.Rd linkcomm/man/graph.feature.Rd linkcomm/man/karate.Rd linkcomm/man/pp_rnapol.Rd linkcomm/man/print.OCG.Rd linkcomm/man/newLinkCommsAt.Rd linkcomm/man/integer.edgelist.Rd linkcomm/man/weighted.Rd linkcomm/man/read.OCG.Rd linkcomm/man/getNestedHierarchies.Rd linkcomm/man/LinkDensities.Rd linkcomm/man/plotOCGraph.Rd linkcomm/man/getAllNestedComm.Rd linkcomm/man/lesmiserables.Rd linkcomm/man/plotLinkCommSumm.Rd linkcomm/man/human_pp.Rd linkcomm/man/plotLinkCommSummComm.Rd linkcomm/man/plotLinkCommDend.Rd linkcomm/man/linkcomm2clustnsee.Rd linkcomm/man/get.community.overlaps.Rd linkcomm/man/meta.communities.Rd linkcomm/man/plotLinkCommMembers.Rd linkcomm/man/getClusterRelatedness.Rd linkcomm/man/get.shared.nodes.Rd linkcomm/man/plot.linkcomm.Rd linkcomm/man/getCommunityConnectedness.Rd linkcomm/man/numberEdgesIn.Rd linkcomm/man/plot.OCG.Rd linkcomm/man/print.linkcomm.Rd linkcomm/man/plotLinkCommGraph.Rd linkcomm/man/corLinkcommCentrality.Rd linkcomm/man/getEdgesIn.Rd linkcomm/man/cutDendrogramAt.Rd linkcomm/man/orderCommunities.Rd linkcomm/man/getCommunityCentrality.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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