In adamsardar/stoneTrees: Solve Node Centric Steiner Tree Problems

library(purrr)
devtools::load_all()

seeds <- V(gene42_igraph)[isTerminal]$name

Calculate all shortest paths : stoneTrees method

I'm just looking how all shortest paths are computed in the package.

calculateAPSPmodule

Compute all shortest path using the same method than the package.

allShortestPaths <- all_shortest_paths(gene42_igraph, from = seeds, to = V(gene42_igraph)[name %in% seeds], mode = "all")$res

How many paths are found ?

length(allShortestPaths)

From ?

Extract 1st node for each paths.

map_chr(allShortestPaths, ~{ .x[1] %>%  as_ids(.) } ) %>% unique

That's where the error is. We want all shortest paths from all nodes to all nodes. It looks like we obtain all shortest paths from the 1st node only.

to ?

Extract last node for each paths.

map_chr(allShortestPaths, ~{ .x[length(.x)] %>% as_ids(.) } ) %>% unique

That looks alright.

Calculate all shortest paths : For all nodes

Compute all shortest paths from all nodes to all nodes.

allShortestPaths2 <-  map(seeds, ~{ all_shortest_paths(gene42_igraph, from = .x, to = V(gene42_igraph)[name %in% seeds], mode = "all")$res } ) %>% unlist(., recursive = FALSE)

How many paths are found ?

length(allShortestPaths2)

many more paths are found.

From ?

Extract 1st node for each paths.

map_chr(allShortestPaths2, ~{ .x[1] %>%  as_ids(.) } ) %>% unique

to ?

Extract last nodefor each paths.

map_chr(allShortestPaths2, ~{ .x[length(.x)] %>% as_ids(.) } ) %>% unique

APSP from all to all

calculateAPSPmoduleForAll <- function(seeds, searchGraph, omitNA = TRUE){

  searchGraphName <- deparse(substitute(searchGraph)) #Capture search graph name

  validateIsNetwork(searchGraph)

  ifelse(omitNA,
         seeds %<>% na.omit(seeds),
         if(any(is.na(V(searchGraph)$name))) warning("NA nodes found in input seed list but 'omitNA' set to FALSE - this can lead to unstable behaviour") )

  seedsNotInGaph <- setdiff(seeds,V(searchGraph)$name)
  seedsInGaph <- intersect(seeds,V(searchGraph)$name)

  if(length(seedsNotInGaph) == length(seeds)){stop("None of the seeds were found in graph!")}
  if(length(seedsNotInGaph) > 0){ warning("Not all seeds found in graph: ",seedsNotInGaph)}

  APSP_vertices <- map(V(searchGraph)[name %in% seedsInGaph], ~{ 


    all_shortest_paths(searchGraph,
                       from = .x,
                       to = V(searchGraph)[name %in% seedsInGaph],
                       mode="all") %>% 
      .$res } ) %>% 
    unlist %>% 
    as.integer %>% 
    unique %>% 
    na.omit

  process_APSP_module <- induced_subgraph(searchGraph,V(searchGraph)[APSP_vertices])

  V(process_APSP_module)$isSeed <- FALSE
  V(process_APSP_module)[name %in% seeds]$isSeed <- TRUE

  process_APSP_module %<>% set_graph_attr("SearchNetwork", searchGraphName)

  return(process_APSP_module)
}

calculateAPSPmoduleForAll(seeds,gene42_igraph)
calculateAPSPmodule(seeds,gene42_igraph)

Another example :

seeds <- V(lymphomaGraph)$name[V(lymphomaGraph)$nodeScore >0]

calculateAPSPmoduleForAll(seeds,lymphomaGraph)

calculateAPSPmodule(seeds,lymphomaGraph)