warship February 2016

R networkD3 package: node coloring in simpleNetwork()

The networkD3 package (https://christophergandrud.github.io/networkD3/ and https://cran.r-project.org/web/packages/networkD3/networkD3.pdf) allows a user to create simple interactive networks (please copy/paste the code below into RStudio):

# Load package
library(networkD3)

# Create fake data
src <- c("A", "A", "A", "A",
        "B", "B", "C", "C", "D")
target <- c("B", "C", "D", "J",
            "E", "F", "G", "H", "I")
networkData <- data.frame(src, target)

# Plot
simpleNetwork(networkData)

Is there a way to specify that I want all elements in the src vector to be a certain color, while allowing all the elements in the target vector to be a different color? This would allow me to visually distinguish src nodes from target nodes in the network.

This functionality doesn't seem to be currently supported in simpleNetwork() (but I'm hoping somebody could help me out with a homebrew script):

enter image description here

A similar but not related question was asked here: specifying colors for each link in a force directed network in networkD3::forceNetwork in R

Answers


jenesaisquoi February 2016

You could do a similar thing as in the linked post, but here is an example using the visNetwork package. This package interfaces with vis.js, and makes really nice interactive graphs.

library(visNetwork)
id <- unique(c(src, target))                                  # node ids
nodes <- data.frame(id, group=+(id %in% src),                 # add a grouping for src/target
  label=id, title=sprintf('<p>Node %s</p>', id))              # add some labels
g <- visNetwork(nodes=nodes, edges=networkData, width="75%")  # make graph
visExport(visHierarchicalLayout(g))                           # make it tree-like

enter image description here


Peter Ellis February 2016

Here's how to control colour of nodes with forceNetwork. Notice this still won't tell you the direction of the links because some nodes are source for some links and target for others - so you'll need to rethink that logic somehow. But anyway, here's controlling colour of nodes.

# Load package
library(networkD3)
library(dplyr) # to make the joins easier

# Create fake data
src <- c("A", "A", "A", "A",
         "B", "B", "C", "C", "D")
target <- c("B", "C", "D", "J",
            "E", "F", "G", "H", "I")
networkData <- data.frame(src, target, stringsAsFactors = FALSE)

nodes <- data.frame(name = unique(c(src, target)), stringsAsFactors = FALSE)
nodes$id <- 0:(nrow(nodes) - 1)


# create a data frame of the edges that uses id 0:9 instead of their names
edges <- networkData %>%
   left_join(nodes, by = c("src" = "name")) %>%
   select(-src) %>%
   rename(source = id) %>%
   left_join(nodes, by = c("target" = "name")) %>%
   select(-target) %>%
   rename(target = id)

edges$width <- 1

# make a grouping variable that will match to colours
nodes$group <- ifelse(nodes$name %in% src, "lions", "tigers")

# simple with default colours
forceNetwork(Links = edges, Nodes = nodes, 
             Source = "source",
             Target = "target",
             NodeID ="name",
             Group = "group",
             Value = "width",
             opacity = 0.9,
             zoom = TRUE)

# control colours with a JS ordinal scale
ColourScale <- 'd3.scale.ordinal()
            .domain(["lions", "tigers"])
           .range(["#FF6900", "#694489"]);'

forceNetwork(Links = edges, Nodes = nodes, 
             Source = "source",
             Target = "target",
             NodeID ="name",
             Group = "group",
             Value = "width",
             opacity = 0.9,
             zoom = TRUE,
             colourScale = JS(ColourScale))

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Asked in February 2016
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