Function to reduce the pathway graph

Description

Function simplifies a pathway graph topology. It merges a user specified nodes into a one. The specified set of nodes must be either a gene family or a protein complex. By a gene family we mean a set of genes with same outgoing or incoming edges. On the other hand, a protein complex is a set of nodes with only undirected binding edges between them and the number of edges is equal to the complex size.

Usage

reduceGraph(graph, reduction)

Arguments

Value

A Pathway

Author(s)

Ivana Ihnatova

Examples

pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")


#gr<-as(pathways,"pathway")
red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("SHC1", "SHC4","SHC2","SHC3"))
reduced<-reduceGraph(pathways, red)
reduced
par(mfrow=c(1,2))

nA<-list(fillcolor=c(NRAS="red", KRAS="red", HRAS="red", SHC1="green", SHC4="green", SHC2="green", SHC3="green"))
plot(as(pathways,"graphNEL"), nodeAttrs=nA, attrs=list(node=list(fontsize=30, height=40)), main="Before")

plot(as(reduced,"graphNEL"), 
 nodeAttrs=list(fillcolor=c(RAS="red", SHC="green")), attrs=list(node=list(fontsize=30, height=40)), main="After")

#this throws an error, "RELA", "FOS","NFKB1" is not correct set of genes
## Not run: 
pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")


gr<-convertIdentifiers(kegg[["Prolactin signaling pathway"]],"SYMBOL")
red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("RELA", "FOS","NFKB1"))
reduced<-reduceGraph(pathways, red)

## End(Not run)

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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> library(ToPASeq)
Loading required package: graphite
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: gRbase
Loading required package: graph
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Rgraphviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ToPASeq/reduceRraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: reduceGraph
> ### Title: Function to reduce the pathway graph
> ### Aliases: reduceGraph
> ### Keywords: manip
> 
> ### ** Examples
> 
> pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
> pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
> 
> 
> #gr<-as(pathways,"pathway")
> red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("SHC1", "SHC4","SHC2","SHC3"))
> reduced<-reduceGraph(pathways, red)
> reduced
"Prolactin signaling pathway" pathway
Native ID           = hsa:04917
Database            = KEGG
Species             = hsapiens
Type of identifiers = SYMBOL
Number of nodes     = 67
Number of edges     = 219
Retrieved on        = 03-05-2016
> par(mfrow=c(1,2))
> 
> nA<-list(fillcolor=c(NRAS="red", KRAS="red", HRAS="red", SHC1="green", SHC4="green", SHC2="green", SHC3="green"))
> plot(as(pathways,"graphNEL"), nodeAttrs=nA, attrs=list(node=list(fontsize=30, height=40)), main="Before")
> 
> plot(as(reduced,"graphNEL"), 
+  nodeAttrs=list(fillcolor=c(RAS="red", SHC="green")), attrs=list(node=list(fontsize=30, height=40)), main="After")
> 
> #this throws an error, "RELA", "FOS","NFKB1" is not correct set of genes
> ## Not run: 
> ##D pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
> ##D pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")
> ##D 
> ##D 
> ##D gr<-convertIdentifiers(kegg[["Prolactin signaling pathway"]],"SYMBOL")
> ##D red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("RELA", "FOS","NFKB1"))
> ##D reduced<-reduceGraph(pathways, red)
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>