ChipScene

library(visNetwork)
library(igraph)
library(scales)
library(ForceAtlas2)

Import Data

import_nodes <- read.csv("MLP chipscene network markdown file.csv", stringsAsFactors = F)
import_edges <- read.csv("MLP chipscene network [Edges].csv", stringsAsFactors = F)

visNetwork

visNetwork with igraphLayout

visN_nodes <- data.frame(
  "id" = import_nodes$Id,
  "label" = import_nodes$Node.label,
  "size" = rescale(import_nodes$r, to = c(5,40))
)

visN_edges <- data.frame(
  "from" = import_edges$Source,
  "to" = import_edges$Target
)

## It doesn't settle like this
## visNetwork(edges = visN_edges, nodes = visN_nodes) 

visNetwork(edges = visN_edges, nodes = visN_nodes) %>%
  visIgraphLayout()

Make igraph object with default layout

chipscene_igraph <- graph.data.frame(d = visN_edges, vertices = visN_nodes)
# V(chipscene_igraph)$name <- visN_nodes$title
plot(chipscene_igraph)

Coerce to visNetwork

visIgraph(chipscene_igraph, idToLabel = F, randomSeed = 1) %>%
  visOptions(highlightNearest = T)

forceAtlas2

The ForceAtlas2 library provides the Force Atlas 2 layout algorithm, the layout.forceatlas2 function is very mouthy and difficult to suppress it’s output (it shows vertex coordinate evolution as the function is iterated). To prevent the output the code chunk has been provided the option include = FALSE and a non-interpreted code chunk is given below instead:

capture.output(forceatlas_layout <- layout.forceatlas2(graph = chipscene_igraph, iterations = 400))

plot(chipscene_igraph, layout = forceatlas_layout)

Coerce to visNetwork, adding some additional iterations to the algorithm:

invisible(
  visN <-
    visIgraph(
      chipscene_igraph,
      idToLabel = F,
      layout = "layout.forceatlas2",
      directed = TRUE,
      iterations = 800,
      randomSeed = 1
    ) %>%
    visOptions(highlightNearest = T)
)

visN