plot_diffnet2: Another way of visualizing diffusion

Description

Another way of visualizing diffusion

Usage

plot_diffnet2(graph, ...)
# S3 method for diffnet
plot_diffnet2(graph, toa, slice = nslices(graph), ...)
# S3 method for default
plot_diffnet2(
  graph,
  toa,
  pers = min(toa, na.rm = TRUE):max(toa, na.rm = TRUE),
  color.ramp = grDevices::colorRamp(viridisLite::magma(20)),
  layout = NULL,
  key.width = 0.1,
  key.args = list(),
  main = "Diffusion dynamics",
  add.map = NULL,
  diffmap.args = list(kde2d.args = list(n = 100)),
  diffmap.alpha = 0.5,
  include.white = "first",
  vertex.size = "degree",
  minmax.relative.size = getOption("diffnet.minmax.relative.size", c(0.01, 0.04)),
  no.graph = FALSE,
  ...
)

Value

A list with the following elements

layout: A numeric matrix with vertex coordinates.
vertex.color: A character vector with computed colors for each vertex.
vertex.label: The value passed to plot_diffnet2.
vertex.shape: A character vector with assigned shapes.
vertex.size: A numeric vector with vertices sizes
diffmap: If add.map=TRUE, the returned values from diffmap

Arguments

graph: Any class of accepted graph format (see netdiffuseR-graphs).
...: Further arguments passed to plot.igraph.
toa: Integer vector of length \(n\) with the times of adoption.
slice: Integer scalar. Number of slice to use as baseline for drawing the graph.
pers: Integer vector of length \(T\) indicating the time periods of the data.
color.ramp: A function as returned by colorRamp.
layout: Passed to plot.igraph.
key.width: Numeric scalar. Sets the proportion of the plot (x-axis) that the key uses.
key.args: List. Further arguments to be passed to drawColorKey.
main: Character scalar. Title of the graph.
add.map: Character scalar. When "first" plots a diffusionMap before the graph itself. If "last" then it adds it at the end. When NULL adds nothing.
diffmap.args: List. If add.map=TRUE, arguments passed to diffusionMap.
diffmap.alpha: Numeric scalar between [0,1]. Alpha level for the map.
include.white: Character scalar. Includes white in the color palette used in the map. When include.white=NULL then it won't include it.
vertex.size: Either a numeric scalar or vector of size \(n\), or any of the following values: "indegree", "degree", or "outdegree" (see details).
minmax.relative.size: Passed to rescale_vertex_igraph.
no.graph: Logical scala. When TRUE the graph is not drawn. This only makes sense when the option add.map is active.

Author

George G. Vega Yon

Details

Plotting is done via the function plot.igraph.

When vertex.size is either of "degree", "indegree", or "outdegree", vertex.size will be replace with dgr(.,cmode = ) so that the vertex size reflects the desired degree.

The argument minmax.relative.size is passed to rescale_vertex_igraph which adjusts vertex.size so that the largest and smallest vertices have a relative size of minmax.relative.size[2] and minmax.relative.size[1] respectively with respect to the x-axis.

If key.width<=0 then no key is created.

By defult, the function passes the following values to plot.igraph: