This package implements the d3-force algorithm developed by Mike Bostock in R, thus providing a way to run many types of particle simulations using its versatile interface.
While the first goal is to provide feature parity with its JavaScript
origin, the intentions is to add more forces, constraints, etc. down the
line. While d3-force is most well-known as a layout engine for
visualising networks, it is capable of much more. Therefore, particles
is provided as a very open framework to play with. Eventually
ggraph
will provide some
shortcut layouts based on particles
with the aim of facilitating
network visualisation.
particles
builds upon the framework provided by
tidygraph
and adds a set of
verbs that defines the simulation:
simulate()
: Creates a simulation based on the input graph, global
parameters, and a genesis function that sets up the initial
conditions of the simulation.wield()
: Adds a force to the simulation. All forces implemented
in d3-force are available as well as some additionals.impose()
: Adds a constraint to the simulation. This function is a
departure from d3-force, as d3-force only allowed for simple fixing
of x and/or y coordinates through the use of the fx and fy
accessors. particles
formalises the use of simulation constraints
and adds new functionalities.evolve()
: Progresses the simulation, either a predefined number
of steps, or until the simulated annealing has cooled down.A recreation of the Les Miserable network in https://bl.ocks.org/mbostock/4062045
library(tidyverse)
library(ggraph)
library(tidygraph)
library(particles)
# Data preparation
d3_col <- c(
'0' = "#98df8a",
'1' = "#1f77b4",
'2' = "#aec7e8",
'3' = "#ff7f0e",
'4' = "#ffbb78",
'5' = "#2ca02c",
'6' = "#d62728",
'7' = "#ff9896",
'8' = "#9467bd",
'9' = "#c5b0d5",
'10' = "#8c564b"
)
raw_data <- 'https://gist.githubusercontent.com/mbostock/4062045/raw/5916d145c8c048a6e3086915a6be464467391c62/miserables.json'
miserable_data <- jsonlite::read_json(raw_data, simplifyVector = TRUE)
miserable_data$nodes$group <- as.factor(miserable_data$nodes$group)
miserable_data$links <- miserable_data$links |>
mutate(from = match(source, miserable_data$nodes$id),
to = match(target, miserable_data$nodes$id))
# Actual particles part
mis_graph <- miserable_data |>
simulate() |>
wield(link_force) |>
wield(manybody_force) |>
wield(center_force) |>
evolve() |>
as_tbl_graph()
# Plotting with ggraph
ggraph(mis_graph, 'nicely') +
geom_edge_link(aes(width = sqrt(value)), colour = '#999999', alpha = 0.6) +
geom_node_point(aes(fill = group), shape = 21, colour = 'white', size = 4,
stroke = 1.5) +
scale_fill_manual('Group', values = d3_col) +
scale_edge_width('Value', range = c(0.5, 3)) +
coord_fixed() +
theme_graph()
#> Warning: Existing variables `x`, `y` overwritten by layout variables
If you intend to follow the steps of the simulation it is possible to attach an event handler that gets called ofter each generation of the simulation. If the handler produces a plot the result will be an animation of the simulation:
# Random overlapping circles
graph <- as_tbl_graph(igraph::erdos.renyi.game(100, 0)) |>
mutate(x = runif(100) - 0.5,
y = runif(100) - 0.5,
radius = runif(100, min = 0.1, 0.2))
# Plotting function
graph_plot <- function(sim) {
gr <- as_tbl_graph(sim)
p <- ggraph(gr, layout = as_tibble(gr)) +
geom_node_circle(aes(r = radius), fill = 'forestgreen', alpha = 0.5) +
coord_fixed(xlim = c(-2.5, 2.5), ylim = c(-2.5, 2.5)) +
theme_graph()
plot(p)
}
# Simulation
graph %>% simulate(velocity_decay = 0.7, setup = predefined_genesis(x, y)) |>
wield(collision_force, radius = radius, n_iter = 2) |>
wield(x_force, x = 0, strength = 0.002) |>
wield(y_force, y = 0, strength = 0.002) |>
evolve(on_generation = graph_plot)
Click here for resulting animation (GitHub don’t allow big gifs in readme)
You can install particles from CRAN using
install.packages("particles")
or alternatively install the development
version from github with:
# install.packages("devtools")
devtools::install_github("thomasp85/particles")
particles
wouldn’t exist and without d3 in general the world would
be a sadder place.manbody_force
and
collision_force
is a modification of the implementation made by
Andrei Kashcha and made
available under MIT license. Big thanks to Andrei as well.Any scripts or data that you put into this service are public.
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