plotNet

Description

Plots the dendrogram and module colors. See ?plotDendroAndColors

Usage

plotNet(object)

Arguments

Value

None.

Author(s)

David L Gibbs

Examples

data(ProCoNA_Data)
#net1 <- buildProconaNetwork("peptide network", peptideData)
plotNet(net1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ProCoNA)
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

Loading required package: flashClust

Attaching package: 'flashClust'

The following object is masked from 'package:fastcluster':

    hclust

The following object is masked from 'package:stats':

    hclust


Attaching package: 'ProCoNA'

The following object is masked from 'package:ProtGenerics':

    peptides

The following object is masked from 'package:Biobase':

    samples

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ProCoNA/plotNet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNet
> ### Title: plotNet
> ### Aliases: plotNet
> 
> ### ** Examples
> 
> data(ProCoNA_Data)
> #net1 <- buildProconaNetwork("peptide network", peptideData)
> plotNet(net1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>