R/get_superstructures.R

In ABAEnrichment: Gene expression enrichment in human brain regions

# get all structures in the hierarchy from a given structure to the root (brain)

get_superstructures=function(structure_id){
    if(length(structure_id)!=1){
        stop("Please use a single structure id.")
    }
    structure_id = as.character(structure_id)
    # remove Allen: string if present
    if(grepl("Allen:", structure_id)){
        struc=strsplit(structure_id,":")[[1]][2]
    } else {
        struc=structure_id  
    }   
    # check if valid structure_id
    if(!(struc %in% daty_strucs[,1])){
        stop(paste("No data for structure_id ",structure_id,".",sep=""))
    }
    # get path
    path=as.character(daty_strucs[daty_strucs[,1]==struc,2])
    path=unlist(strsplit(path,"/"))
    # remove empty (first) entry
    path=path[path!=""]
    # add Allen: string again if it was in input    
    if(grepl("Allen:", structure_id)){
        path=paste("Allen:",path,sep="")
    }
#   # turn around, to go frome from current node to root
#   path=rev(path)
    return(path)
}