cluster: Network clustering

In ProNet: Biological Network Construction, Visualization and Analyses

Description

Network clustering based on different methods.

Usage

cluster(graph, method = c("FN", "MCL", "LINKCOMM", "MCODE"), expansion = 2,
  inflation = 2, hcmethod = "average", directed = FALSE, outfile = NULL,
  plot = TRUE, layout = c("reingold.tilford", "circle", "random",
  "fruchterman.reingold", "sphere", "kamada.kawai", "lgl"), ...)

Arguments

graph	An igraph object.
method	Clustering method, possible values are FN, MCL, LINKCOMM and MCODE.
expansion	Numeric value > 1 for the expansion parameter, if method is MCL. See MCL for more information.
inflation	Numeric value > 0 for the inflation power coefficient, if method is MCL. See MCL for more information.
hcmethod	A character string naming the hierarchical clustering method to use. Default value is average. See linkcomm for more information.
directed	Logical value, indicating whether the network is directed (if TRUE) or not (if FLASE).
outfile	File to save the clustering result.
plot	Logical value, indicating whether to plot summary output (if TRUE) or not (if FLASE).
layout	Mode of the layout, possible values are fruchterman.reingold, reingold.tilford, random, circle, kamada.kawai, lgl and sphere. See igraph for more information.
...	Other arguments.

Value

A summary and visulization of the clustering.

References

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.

See Also

mcode

Examples

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")

Example output

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 

ProNet documentation built on May 30, 2017, 2:02 a.m.