Last data update: 2014.03.03

R: Class "coloredGraph"
coloredGraph-classR Documentation

Class "coloredGraph"

Description

a graph to which color attributes have been attached

Objects from the Class

Objects can be created by calls of the form new("coloredGraph", nodes, edgeL, edgemode). these are graphNEL instances with some additional graphData

Slots

nodes:

Object of class "vector" ~~

edgeL:

Object of class "list" ~~

edgeData:

Object of class "attrData" ~~

nodeData:

Object of class "attrData" ~~

renderInfo:

Object of class "renderInfo" ~~

graphData:

Object of class "list" ~~

Extends

Class "graphNEL-class", directly. Class "graph-class", by class "graphNEL", distance 2.

Methods

plot

signature(x = "coloredGraph"): ...

Examples

showClass("coloredGraph")
example(randomGraph)
nn = nodes(g1)
x = runif(length(nn))
names(x) = nn
h1 = colorNodes(g1, x, colorRampPalette(brewer.pal(9, "Blues"))(length(nn)),
 pwayRendAttrs)
h1
plot(h1)

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(pathRender)
Loading required package: graph
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: Rgraphviz
Loading required package: grid
Loading required package: RColorBrewer
Loading required package: cMAP
Loading required package: AnnotationDbi
Loading required package: stats4
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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    from, to

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pathRender/coloredGraph-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coloredGraph-class
> ### Title: Class "coloredGraph"
> ### Aliases: coloredGraph-class pwayRendAttrs plot,coloredGraph,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("coloredGraph")
Class "coloredGraph" [package "pathRender"]

Slots:
                                                                        
Name:       nodes      edgeL   edgeData   nodeData renderInfo  graphData
Class:     vector       list   attrData   attrData renderInfo       list

Extends: 
Class "graphNEL", directly
Class "graph", by class "graphNEL", distance 2
Class "graphBase", by class "graphNEL", distance 3
> example(randomGraph)

rndmGr>  set.seed(123)

rndmGr>  V <- letters[1:10]

rndmGr>  M <- 1:4

rndmGr>  g1 <- randomGraph(V, M, 0.2)

rndmGr>  numEdges(g1) # 16, in this case
[1] 16

rndmGr>  edgeNames(g1)# "<from> ~ <to>"  since undirected
 [1] "a~b" "a~d" "a~e" "a~f" "a~h" "b~f" "b~d" "b~e" "b~h" "c~h" "d~e" "d~f"
[13] "d~h" "e~f" "e~h" "f~h"
> nn = nodes(g1)
> x = runif(length(nn))
> names(x) = nn
> h1 = colorNodes(g1, x, colorRampPalette(brewer.pal(9, "Blues"))(length(nn)),
+  pwayRendAttrs)
> h1
A coloredGraph graph with undirected edges
Number of Nodes = 10 
Number of Edges = 16 
> plot(h1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>