Description Usage Arguments Value References See Also Examples
Network clustering based on different methods.
1 2 3 4 |
graph |
An igraph object. |
method |
Clustering method, possible values are |
expansion |
Numeric value > 1 for the expansion parameter, if |
inflation |
Numeric value > 0 for the inflation power coefficient, if |
hcmethod |
A character string naming the hierarchical clustering method to use. Default value is |
directed |
Logical value, indicating whether the network is directed (if |
outfile |
File to save the clustering result. |
plot |
Logical value, indicating whether to plot summary output (if |
layout |
Mode of the layout, possible values are |
... |
Other arguments. |
A summary and visulization of the clustering.
A Clauset, MEJ Newman, C (2004) Moore: Finding community structure in very large networks, http://www.arxiv.org/abs/cond-mat/0408187.
van Dongen, S.M. (2000) Graph Clustering by Flow Simulation. Ph.D. thesis, Universtiy of Utrecht.
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 (14), 2011-2012.
Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003 Jan 13;4(1):2.
1 2 3 4 | nlocal<-data.frame(c("DVL1","DVL2","DVL3"))
net<-construction(input=nlocal,db="HPRD",species="human",ID.type="Gene symbol",hierarchy=1)
cluster(net,method="MCODE",layout="fruchterman.reingold")
cluster(net,method="FN",layout="fruchterman.reingold")
|
Loading required package: Rcpp
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: MCL
Loading required package: linkcomm
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"))
SMAD7 PRKCA DAB2 RUNX2 SMAD4 SMAD2 SMAD3 ATN1
2 1 2 2 2 2 2 1
RHOA DAAM1 - RAC1 PPM1A BAG3 PITX1 AXIN1
2 2 1 2 2 1 2 2
ARR3 TP53 EPS8 AP1M1 CSNK1E PRKCB CSNK2A1 PPP2CA
2 2 2 2 2 2 2 2
PRKCG PARD6A TRAF2 SNIP1 DVL1 DVL2 MCRS1 CSNK1D
2 1 2 2 2 2 1 2
U2AF2 MYST2 HECW1 TIFA SMURF1 BRD7 SNF8 AP2M1
2 2 2 2 2 2 1 2
TCEB3B DYNLT1 DVL3 ZNF408 FRAT1 CXXC4 VANGL1 SORBS3
2 2 2 2 2 2 2 1
CTNNB1 FZD4 RNPS1 LNX1 CCNK THAP1 ARRB1 ARRB2
2 1 1 2 0 2 2 1
PCBD1 ZBTB48 RHOXF2 ZNF165 USP5 USP13 ZNF263 PRPF3
2 2 1 1 1 2 1 2
CCDC33 $ZBTB8$ RBPMS BAHD1 C16orf48 DPPA2 KLHL12 ZNF250
2 2 0 1 2 2 2 2
MARK2 VANGL2 LY6H CCDC88C POLI CPSF7 C20orf158 TNFAIP8L1
2 2 0 2 1 1 0 0
SNX22 C9orf100 DDI1 FAM105B NKD1 HDHD2
2 2 1 1 0 0
SMAD7 PRKCA DAB2 RUNX2 SMAD4 SMAD2 SMAD3 ATN1
4 2 5 4 4 4 4 2
RHOA DAAM1 - RAC1 PPM1A BAG3 PITX1 AXIN1
2 2 2 2 4 3 2 4
ARR3 TP53 EPS8 AP1M1 CSNK1E PRKCB CSNK2A1 PPP2CA
4 4 4 1 4 5 4 4
PRKCG PARD6A TRAF2 SNIP1 DVL1 DVL2 MCRS1 CSNK1D
5 5 1 4 4 3 2 4
U2AF2 MYST2 HECW1 TIFA SMURF1 BRD7 SNF8 AP2M1
3 1 4 1 2 2 3 3
TCEB3B DYNLT1 DVL3 ZNF408 FRAT1 CXXC4 VANGL1 SORBS3
3 3 1 1 4 4 1 3
CTNNB1 FZD4 RNPS1 LNX1 CCNK THAP1 ARRB1 ARRB2
4 3 3 1 2 3 3 3
PCBD1 ZBTB48 RHOXF2 ZNF165 USP5 USP13 ZNF263 PRPF3
1 1 2 3 3 4 3 1
CCDC33 $ZBTB8$ RBPMS BAHD1 C16orf48 DPPA2 KLHL12 ZNF250
1 1 2 1 2 3 1 3
MARK2 VANGL2 LY6H CCDC88C POLI CPSF7 C20orf158 TNFAIP8L1
5 4 1 4 3 3 1 1
SNX22 C9orf100 DDI1 FAM105B NKD1 HDHD2
1 2 3 3 1 4
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.