produce list of vectors of (shortest) paths from root to all nodes in gr

Usage

graph2paths(gr, root = "http://www.ifomis.org/bfo/1.1#Entity", excise = NULL)

Arguments

gr: graphNEL (package graph) instance representing an ontology
root: character(1) node from which to produce paths
excise: character() or NULL, path steps to exclude

Examples

if (!requireNamespace("graph")) stop("install graph package from Bioconductor to use this function")
jpath = system.file("json", "aut.json.gz", package="ontoProc")
cg = jowl2classgraph(jpath,
  dropstrings = "http://purl.org/autism-ontology/1.0/autism-rules.owl#")
evec = grep("span\\#|snap\\#", graph::nodes(cg), value=TRUE)
paths = graph2paths(cg, excise=evec)
tail(paths)
#> [[1]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"           
#> [2] "Autism Phenotype"                               
#> [3] "Personal Traits"                                
#> [4] "Cognitive Ability"                              
#> [5] "Abstract Thinking"                              
#> [6] "Imagination"                                    
#> [7] "Imaginative Play With Peers"                    
#> [8] "Some Play With Other Children BUT No Pretending"
#> 
#> [[2]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"
#> [2] "Autism Phenotype"                    
#> [3] "Personal Traits"                     
#> [4] "Executive Function"                  
#> [5] "Planning"                            
#> [6] "Preparing forPreparing Tasks"        
#> 
#> [[3]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"                  
#> [2] "Autism Phenotype"                                      
#> [3] "Personal Traits"                                       
#> [4] "Stereotyped Restricted and Repetitive Behavior"        
#> [5] "Restricted and Repetitive Behavior"                    
#> [6] "Restricted and Unusual Interests"                      
#> [7] "Circumscribed Interests"                               
#> [8] "Circumscribed InterestsCircumscribed UnknownOrNotAsked"
#> 
#> [[4]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"
#> [2] "Autism Phenotype"                    
#> [3] "Social Competence"                   
#> [4] "Recognition of Social Norms"         
#> [5] "Intentional BadIntentional Behavior" 
#> 
#> [[5]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"                            
#> [2] "Autism Phenotype"                                                
#> [3] "Social Competence"                                               
#> [4] "Interpersonal Interactions"                                      
#> [5] "Reciprocal SocialReciprocal Interaction"                         
#> [6] "Joint Attention"                                                 
#> [7] "Seeking To Share herHis Enjoyment With Others"                   
#> [8] "Seeking To Share herHis Enjoyment With Others NotKnownOrNotAsked"
#> 
#> [[6]]
#> [1] "http://www.ifomis.org/bfo/1.1#Entity"
#>