plot_diffnet2: Another way of visualizing diffusion

In srdyal/diffusiontest: Analysis of Diffusion and Contagion Processes on Networks

Another way of visualizing diffusion

Description

Another way of visualizing diffusion

Usage

plot_diffnet2(graph, ...)

## S3 method for class 'diffnet'
plot_diffnet2(graph, toa, slice = nslices(graph), ...)

## Default S3 method:
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,
  ...
)

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.

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:

• vertex.label equals to ""

• vertex.frame.color equals to "white"

• add equals to TRUE

• rescale equals to FALSE

• vertex.size equals to rescale.fun(vertex.size)

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

Author(s)

George G. Vega Yon

See Also

Other visualizations: dgr(), diffusionMap(), drawColorKey(), grid_distribution(), hazard_rate(), plot_adopters(), plot_diffnet(), plot_infectsuscep(), plot_threshold(), rescale_vertex_igraph()

srdyal/diffusiontest documentation built on Sept. 2, 2023, 2:49 p.m.