How to define the difference between id's nodes of graph?

Question

I have a graph g

n = 8
m <- t(matrix(c(
0,0,0,0,0,0,0,8,
3,0,0,0,0,0,0,0,
5,0,0,5,1,0,0,0,
0,0,6,0,0,7,1,0,
0,6,2,0,0,0,0,0,
0,0,0,0,0,0,0,0,
7,4,0,0,8,0,0,3,
0,3,0,0,0,9,0,0),ncol=n))

library(igraph)

g <- graph_from_adjacency_matrix(m, weighted=TRUE, mode="directed")
V(g1)$name <-  letters[1:n]

After some calculation I have the vector str with vertex's names:

str <- c("dca", "dgb", "dc",  NA,  "dce", "df",   "dg",   "dg")

I need to find the unique nodes and plot a tree where root node is the first symbol in str.

My attempt is:

str[is.na(str)]<-""; 
vname <- noquote(unique(strsplit((paste0(str, collapse="")),"")[[1]]))
vname
# d c a g b e f

vid <- match( vname, V(g1)$name )
vid
# 4 3 1 7 2 5 6

One can see that the difference between nodes of g and vid is the h node, its id is 8.

Expected result is:

Question. How to define the difference in id's nodes and delete vertices with corresponding edges to plot a tree?

user_12148402 · Answer

You can use subgraph.edges:

# find wanted edges
str <- unique(str[!is.na(str)])
keep_edges <- apply(
  X = unique(
    do.call(rbind, lapply(strsplit(str, ""), function(x) embed(x, 2)[,2:1]))
  ),
  MARGIN = 1,
  paste0,
  collapse = "|"
)

# subgraph containing only wanted edges 
g <- subgraph.edges(g1, keep_edges)
nodes <- V(g)$name

plot(g, layout = igraph::layout_as_tree)

user_12158757 · Answer

You can use eval + graph_from_literal + gsub to create a graph object g like below

tryCatch({
    if (all(is.na(str))) warning("All NAs in the input array!")
    g <- eval(
        str2lang(
            sprintf(
                "graph_from_literal(%s)",
                toString(gsub("(?<=.)(?=.)", "-+", na.omit(str), perl = TRUE))
            )
        )
    )
})

and you will see

> g
IGRAPH fe5b7ea DN-- 7 6 -- 
+ attr: name (v/c)
+ edges from fe5b7ea (vertex names):
[1] d->c d->g d->f c->a c->e g->b

and plot(g, layout = layout_as_tree) gives

How to define the difference between id's nodes of graph?

2 Answers