plotRegulatoryGraph: This function layouts a regulatory graph and plots it using...

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function takes a regulatory graph as generated by pathway2regulatoryGraph and plots it using standard layout options of layoutRegulatoryGraph. This function is a wrapper for layoutRegulatoryGraph with standard parameters. Subgraphs can be painted with different colors. This can be done by passing parameter subgraph a list of character vectors with node names.

Usage

plotRegulatoryGraph(mygraph, subgraphs = list(), layoutGraph = TRUE)

Arguments

mygraph	graphNEL, regulatory graph
subgraphs	list of character vectors with node names
layoutGraph	logical. If FALSE the graph is not laid out again but send directly to Rgraphviz::renderGraph.

Value

none

Author(s)

Frank Kramer

Examples

 # load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pwid2 = "pid_p_100146_hespathway"
 mygraph = pathway2RegulatoryGraph(biopax, pwid1)
 plotRegulatoryGraph(mygraph)

Example output

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

Found 23 pathway components. Putting them together...
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P36 Controlleds:  P29
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P29 Controlleds:  P28 P26 P11
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P40 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P36 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P40 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P37 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P15 Controlleds:  P30
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P14 Controlleds:  P30
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P30 Controlleds:  P10 P25 P33 P12 P11 P13
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P32 Controlleds:  P10 P25 P33 P12
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P27
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P27
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P17
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P17
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P18
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P18
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P31 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P21 P20 P19 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P38 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P39 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P21 P20 P19 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P38 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P35 Controlleds:  P20 P19 P21
There were 19 warnings (use warnings() to see them)
Loading required package: Rgraphviz
Loading required package: grid

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.