pathway2Graph: This function generates a directed graph from all the...
In rBiopaxParser: Parses BioPax files and represents them in R

Description Usage Arguments Value Author(s) Examples

This function generates a directed graph from all the interactions of a specified pathway in a biopax model. Edges with no direction are indicated by a 0 weight.

pathway2Graph(
  biopax,
  pwid,
  expandSubpathways = TRUE,
  splitComplexMolecules = FALSE,
  useIDasNodenames = TRUE,
  verbose = FALSE,
  withDisconnectedParts = TRUE
)

`biopax`	A biopax model
`pwid`	string
`expandSubpathways`	logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
`splitComplexMolecules`	logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges. Default value is FALSE
`useIDasNodenames`	logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
`verbose`	logical
`withDisconnectedParts`	logical. If TRUE the pathway graph is returned as such, else only the largest connected component is given back

Returns the a graph object of the specified pathway. Edges with no direction are indicated by a 0 weight.

Nirupama Benis

 # load data
data(biopaxLevel3Example) # location of the data
pwid <- "Pathway1019"
# build pathway using pathway2Graph
pathwayAsGraph <- pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE, useIDasNodenames = TRUE, verbose = FALSE, withDisconnectedParts = TRUE)
pathwayAsGraph # should have 23 nodes, 24 edges
plotRegulatoryGraph(pathwayAsGraph)
# build pathway discarding the disconnected parts of the graph
pathwayAsGraph <- pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE, useIDasNodenames = TRUE, verbose = FALSE, withDisconnectedParts = FALSE)
pathwayAsGraph # should have 10 nodes, 11 edges
plotRegulatoryGraph(pathwayAsGraph)

Loading required package: data.table
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'graph'

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

    combineNodes

Warning messages:
1: In pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE,  :
  Problem while adding edge (weight = 1) to graph: Edge already exists between Complex4242 and PhysicalEntity567 (weight = (opposite direction)). Skipping this edge.
2: In .local(from, to, graph) : edges replaced: 'Complex4238|Complex4239'
3: In pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE,  :
  Problem while adding edge (weight = 1) to graph: Edge already exists between Complex4242 and PhysicalEntity567 (weight = (opposite direction)). Skipping this edge.
4: In .local(from, to, graph) : edges replaced: 'Complex4242|Complex4244'
A graphNEL graph with directed edges
Number of Nodes = 23 
Number of Edges = 24 
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: igraph

Attaching package: 'igraph'

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

    degree, edges, intersection, union

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

    normalize, path, union

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

    decompose, spectrum

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

    union

Warning messages:
1: In pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE,  :
  Problem while adding edge (weight = 1) to graph: Edge already exists between Complex4242 and PhysicalEntity567 (weight = (opposite direction)). Skipping this edge.
2: In .local(from, to, graph) : edges replaced: 'Complex4238|Complex4239'
3: In pathway2Graph(biopax = biopaxLevel3Example, pwid = pwid, splitComplexMolecules = FALSE,  :
  Problem while adding edge (weight = 1) to graph: Edge already exists between Complex4242 and PhysicalEntity567 (weight = (opposite direction)). Skipping this edge.
4: In .local(from, to, graph) : edges replaced: 'Complex4242|Complex4244'
A graphNEL graph with directed edges
Number of Nodes = 10 
Number of Edges = 11