R/internal_props_node.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

internal_props_node<-
  function(){
    #' @keywords internal
    
    node_props<-
      data.frame(shape=
                   c(Protein="rectangle"
                     ,Complex="rectangle"
                     ,SmallMolecule="rectangle"
                     ,PhysicalEntity="rectangle"
                     ,RNA="rectangle"
                     ,DNA="rectangle"
                     ,Pathway="oval"
                     
                     ,BiochemicalReaction="circle"
                     ,TemplateReaction="circle"
                     ,ComplexAssembly="circle"
                     ,Transport="circle"
                     ,TransportWithBiochemicalReaction="circle"
                     ,Degradation="circle"
                     
                     ,dbid="rectangle"
                     
                     ,CellularLocation="component"
                     ,SequenceModification="component"
                     ,Evidence="component"
                     ,Interaction="component"
                     ,RelationshipType="component")
                 ,fillcolor=
                   c(Protein="deepskyblue1"
                     ,Complex="mediumpurple3"
                     ,SmallMolecule="gold1"
                     ,PhysicalEntity="lightgray"
                     ,RNA="salmon1"
                     ,DNA="mediumorchid1"
                     ,Pathway="blue1"
                     
                     ,BiochemicalReaction="orange1"
                     ,TemplateReaction="firebrick1"
                     ,ComplexAssembly="steelblue3"
                     ,Transport="limegreen"
                     ,TransportWithBiochemicalReaction="orange1"
                     ,Degradation="darkgray"
                     
                     ,dbid="white"
                     
                     ,CellularLocation="yellowgreen"
                     ,SequenceModification="yellowgreen"
                     ,Evidence="yellowgreen"
                     ,Interaction="yellowgreen"
                     ,RelationshipType="yellowgreen")
                 ,color=
                   c(Protein="deepskyblue1"
                     ,Complex="mediumpurple3"
                     ,SmallMolecule="gold1"
                     ,PhysicalEntity="lightgray"
                     ,RNA="salmon1"
                     ,DNA="mediumorchid1"
                     ,Pathway="blue1"
                     
                     ,BiochemicalReaction="orange1"
                     ,TemplateReaction="firebrick1"
                     ,ComplexAssembly="steelblue3"
                     ,Transport="limegreen"
                     ,TransportWithBiochemicalReaction="limegreen"
                     ,Degradation="darkgray"
                     
                     ,dbid="black"
                     
                     ,CellularLocation="olivedrab"
                     ,SequenceModification="olivedrab"
                     ,Evidence="olivedrab"
                     ,Interaction="olivedrab"
                     ,RelationshipType="olivedrab")
                 ,fontcolor=
                   c(Protein="gray20"
                     ,Complex="whitesmoke"
                     ,SmallMolecule="gray20"
                     ,PhysicalEntity="gray20"
                     ,RNA="gray20"
                     ,DNA="gray20"
                     ,Pathway="whitesmoke"
                     
                     ,BiochemicalReaction="gray20"
                     ,TemplateReaction="whitesmoke"
                     ,ComplexAssembly="whitesmoke"
                     ,Transport="gray20"
                     ,TransportWithBiochemicalReaction="gray20"
                     ,Degradation="whitesmoke"
                     
                     ,dbid="gray50"
                     
                     ,CellularLocation="gray50"
                     ,SequenceModification="gray50"
                     ,Evidence="gray50"
                     ,Interaction="gray50"
                     ,RelationshipType="gray50")
                 # ,style=
                 #     c(Protein="solid"
                 #       ,Complex="solid"
                 #       ,SmallMolecule="solid"
                 #       ,PhysicalEntity="solid"
                 #       ,RNA="solid"
                 #       ,DNA="solid"
                 #       ,Pathway="solid"
                 #       
                 #       ,BiochemicalReaction="solid"
                 #       ,TemplateReaction="solid"
                 #       ,ComplexAssembly="solid"
                 #       ,Transport="solid"
                 #       ,TransportWithBiochemicalReaction="bold"
                 #       ,Degradation="solid"
                 #       
                 #       ,dbid="solid"
                 #       
                 #       ,CellularLocation="solid"
                 #       ,SequenceModification="solid"
                 #       ,Evidence="solid"
                 #       ,Interaction="solid"
                 #       ,RelationshipType="solid")
                 ,penwidth=
                   c(Protein=1
                     ,Complex=1
                     ,SmallMolecule=1
                     ,PhysicalEntity=1
                     ,RNA=1
                     ,DNA=1
                     ,Pathway=1
                     
                     ,BiochemicalReaction=1
                     ,TemplateReaction=1
                     ,ComplexAssembly=1
                     ,Transport=1
                     ,TransportWithBiochemicalReaction=1
                     ,Degradation=1
                     
                     ,dbid=1
                     
                     ,CellularLocation=1
                     ,SequenceModification=1
                     ,Evidence=1
                     ,Interaction=1
                     ,RelationshipType=1)
                 ,peripheries=
                   c(Protein=1
                     ,Complex=1
                     ,SmallMolecule=1
                     ,PhysicalEntity=1
                     ,RNA=1
                     ,DNA=1
                     ,Pathway=1
                     
                     ,BiochemicalReaction=1
                     ,TemplateReaction=1
                     ,ComplexAssembly=1
                     ,Transport=1
                     ,TransportWithBiochemicalReaction=1
                     ,Degradation=1
                     
                     ,dbid=1
                     
                     ,CellularLocation=1
                     ,SequenceModification=1
                     ,Evidence=1
                     ,Interaction=1
                     ,RelationshipType=1)
                 ,tooltip=
                   c(Protein="Protein"
                     ,Complex="Complex"
                     ,SmallMolecule="Small Molecule"
                     ,PhysicalEntity="Physical Entity"
                     ,RNA="RNA"
                     ,DNA="DNA"
                     ,Pathway="Pathway"
                     
                     ,BiochemicalReaction="Biochemical Reaction"
                     ,TemplateReaction="Template Reaction"
                     ,ComplexAssembly="Complex Assembly"
                     ,Transport="Transport"
                     ,TransportWithBiochemicalReaction="Transport with Biochemical Reaction"
                     ,Degradation="Degradation"
                     
                     ,dbid="ID"
                     ,CellularLocation="Cellular Location"
                     ,SequenceModification="Sequence Modification"
                     ,Evidence="Evidence"
                     ,Interaction="Interaction"
                     ,RelationshipType="Relationship Type")
                 ,fixedsize=
                   c(Protein=FALSE
                     ,Complex=FALSE
                     ,SmallMolecule=FALSE
                     ,PhysicalEntity=FALSE
                     ,RNA=FALSE
                     ,DNA=FALSE
                     ,Pathway=FALSE
                     
                     ,BiochemicalReaction=TRUE
                     ,TemplateReaction=TRUE
                     ,ComplexAssembly=TRUE
                     ,Transport=TRUE
                     ,TransportWithBiochemicalReaction=TRUE
                     ,Degradation=TRUE
                     
                     ,dbid=FALSE
                     
                     ,CellularLocation=FALSE
                     ,SequenceModification=FALSE
                     ,Evidence=FALSE
                     ,Interaction=FALSE
                     ,RelationshipType=FALSE)
                 ,height=
                   c(Protein=NA
                     ,Complex=NA
                     ,SmallMolecule=NA
                     ,PhysicalEntity=NA
                     ,RNA=NA
                     ,DNA=NA
                     ,Pathway=NA
                     
                     ,BiochemicalReaction=0.5
                     ,TemplateReaction=0.5
                     ,ComplexAssembly=0.5
                     ,Transport=0.5
                     ,TransportWithBiochemicalReaction=0.5
                     ,Degradation=0.5
                     
                     ,dbid=NA
                     
                     ,CellularLocation=NA
                     ,SequenceModification=NA
                     ,Evidence=NA
                     ,Interaction=NA
                     ,RelationshipType=NA)
                 ,width=
                   c(Protein=NA
                     ,Complex=NA
                     ,SmallMolecule=NA
                     ,PhysicalEntity=NA
                     ,RNA=NA
                     ,DNA=NA
                     ,Pathway=NA
                     
                     ,BiochemicalReaction=0.5
                     ,TemplateReaction=0.5
                     ,ComplexAssembly=0.5
                     ,Transport=0.5
                     ,TransportWithBiochemicalReaction=0.5
                     ,Degradation=0.5
                     
                     ,dbid=NA
                     
                     ,CellularLocation=NA
                     ,SequenceModification=NA
                     ,Evidence=NA
                     ,Interaction=NA
                     ,RelationshipType=NA))
    
    node_props<-
      node_props %>% 
      cbind(type=rownames(.)
            ,.)
    return(node_props)
  }