Last data update: 2014.03.03

R: Compute an Adjacency Matrix for a graphBAM object
adjacencyMatrixR Documentation

Compute an Adjacency Matrix for a graphBAM object

Description

Though unwieldy for large matrices, a full adjacency matrix can be useful for debugging and export.

If the graph is “undirected” then recicprocal edges are explicit in the matrix.

Usage

adjacencyMatrix(object)

Arguments

object

A graphBAM object.

Details

Thus far only implemented for graphBAM objects.

Value

adjacencyMatrix returns an n x n matrix, where n is the number of nodes in the graph, ordered in the same manner as seen in the nodes method. All cells in the matrix are 0 except where edges are found.

Author(s)

P. Shannon

See Also

edgeMatrix

Examples

  from   <- c("a", "a", "a", "x", "x", "c")
  to     <- c("b", "c", "x", "y", "c", "a")
  weight <- c(3.4, 2.6, 1.7, 5.3, 1.6, 7.9)
  df <- data.frame(from, to, weight)
  g1 <- graphBAM(df, edgemode = "directed")
  adjacencyMatrix(g1)

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)

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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(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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/graph/adjacencyMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: adjacencyMatrix
> ### Title: Compute an Adjacency Matrix for a graphBAM object
> ### Aliases: adjacencyMatrix adjacencyMatrix,graphBAM-method
> ### Keywords: manip
> 
> ### ** Examples
> 
>   from   <- c("a", "a", "a", "x", "x", "c")
>   to     <- c("b", "c", "x", "y", "c", "a")
>   weight <- c(3.4, 2.6, 1.7, 5.3, 1.6, 7.9)
>   df <- data.frame(from, to, weight)
>   g1 <- graphBAM(df, edgemode = "directed")
>   adjacencyMatrix(g1)
  a b c x y
a 0 1 1 1 0
b 0 0 0 0 0
c 1 0 0 0 0
x 0 0 1 0 1
y 0 0 0 0 0
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>