# install.packages("igraph")
# install.packages("tidygraph")

terms_labels <- read.csv("terms_labels.csv", header=TRUE)
head(terms_labels)

library(dplyr)

terms_labels$uri %<>% as.character() %>% strsplit("/", fixed=TRUE) %>% sapply(tail, 1)
terms_labels$narrower...uri %<>% as.character() %>% strsplit("/", fixed=TRUE) %>% sapply(tail, 1) %>% sapply(function(x) if(identical(x,character(0))) NA else x)
terms_labels$broader...uri %<>% as.character() %>% strsplit("/", fixed=TRUE) %>% sapply(tail, 1) %>% sapply(function(x) if(identical(x,character(0))) NA else x)
terms_labels %<>% select(uri,broader...uri,narrower...uri,pref.label,class) %>% rename(ID=uri,broader_ID=broader...uri,narrower_ID=narrower...uri,idmsClass=class) %>% transform(ID = as.numeric(ID), broader_ID = as.numeric(broader_ID), narrower_ID = as.numeric(narrower_ID), pref.label = as.character(pref.label), idmsClass = as.character(idmsClass))
head(terms_labels)

terms_labels_subclass <- terms_labels %>% filter(idmsClass=="TPG")
broader <- terms_labels_subclass %>% subset(select=c("broader_ID", "ID")) %>% na.omit() %>% unique() %>% rename(from=broader_ID,to=ID)
narrower <- terms_labels_subclass %>% subset(select=c("ID", "narrower_ID")) %>% na.omit() %>% unique() %>% rename(from=ID,to=narrower_ID)
edgelist <- broader %>% rbind(narrower) %>% unique()
head(edgelist)

library(tidygraph)
library(igraph)
g <- edgelist %>% as_tbl_graph(directed=TRUE)
g
print(paste0("# of edges: ",  gsize(g)," | # of nodes: ", gorder(g), " | # of weakly connected components: ", length(decompose(g, mode="weak"))))

options(repr.plot.width=10, repr.plot.height=10)
g %>% plot(layout=layout.fruchterman.reingold, vertex.size=degree(g)*0.6, vertex.label.color="darkblue", vertex.label.cex=0.6, vertex.color="orange", edge.arrow.size=0.1, edge.width=0.5, edge.color="gray")

options(repr.plot.width=5, repr.plot.height=4)
example <- create_tree(6, children=3) %>% mutate(name = letters[1:6]) 
# example %>% plot(layout=layout.reingold.tilford,vertex.label.cex=1, vertex.size=40)
library(IRdisplay)
display_png(file="igraphTraversalExample.PNG")

example %>% mutate(rank = map_bfs_int(node_is_root(), .f = function(rank, ...) {
rank
})) 

example %>% mutate(rank = map_dfs_int(node_is_root(), .f = function(rank, ...) {
rank
})) 

which(V(g) %>% sapply(function(x) neighbors(g,x,mode="in")) %>% sapply(length) == 0)

g %>% mutate(depth = bfs_dist(
    which(V(g) %>% sapply(function(x) neighbors(g,x,mode="in")) %>% sapply(length) == 0)
                          ))

g %>% mutate(neighborhood_in_edges = map_local_dbl(mode="in", .f = function(neighborhood, ...) {
    gsize(neighborhood)
    })) %>% mutate(depth = bfs_dist(which(neighborhood_in_edges==0))) %>% arrange(neighborhood_in_edges)

options(repr.plot.width=10, repr.plot.height=5)
par(mfrow = c(1, 2))
g %>% plot(layout=layout.kamada.kawai,vertex.size=degree(g)*1.2, vertex.label.color="darkblue", vertex.label.cex=0.6, vertex.color="orange", edge.arrow.size=0.1, edge.width=0.5, edge.color="gray")
mtext("Kamada Kawai layout") 
g %>% plot(layout=layout.reingold.tilford, vertex.size=10, vertex.label.color="darkblue", vertex.label.cex=0.6, vertex.color="orange", edge.arrow.size=0.2, edge.width=1, edge.color="darkgray")
mtext("Reingold & Tilford’s Tidier layout") 

class_names = c("CTP", "NAME", "ID", "LEG", "SIT", "TPG", "ORG")
results = data.frame()

for(i in class_names){
    
    terms_labels_subclass <- terms_labels %>% filter(idmsClass==i)
    broader <- terms_labels_subclass %>% subset(select=c("broader_ID", "ID")) %>% na.omit() %>% unique() %>% rename(from=broader_ID,to=ID)
    narrower <- terms_labels_subclass %>% subset(select=c("ID", "narrower_ID")) %>% na.omit() %>% unique() %>% rename(from=ID,to=narrower_ID)
    edgelist <- broader %>% rbind(narrower) %>% unique()
    g <- edgelist %>% as_tbl_graph(directed=TRUE)
    
    numVertex <- gorder(g)
    numEdge <- gsize(g)
    numComponents <- length(decompose(g, mode="weak"))
    
    if(numComponents == 1) {
        indegree <- V(g) %>% sapply(function(x) neighbors(g,x,mode="in")) %>% sapply(length)
        root <- names(which(indegree == 0))
    }
    else {
        root = NA
    }
    
    row <- data.frame(i, numVertex, numEdge, numComponents, root)
    results <- rbind(results, row)
}

colnames(results) <- c("Class", "Vertices", "Edges", "Components", "Root")
results