plot_ellipses: Plot network of nodes and ellipses

In mrc-ide/PlasmoMAPI: Mapping Plasmodium Spatial Connectivity from Genetic Data

Description

Produce a simple plot of nodes connected by all pairwise ellipses, where nodes make up the foci of ellipses and colours correspond to statistical distances. Edges with NA values are not plotted.

Usage

plot_ellipses(
  proj,
  eccentricity = 0.9,
  n = 30,
  alpha = 0.4,
  col_scale = rev(PlasmoMAPI::col_hotcold()),
  zlim = NULL,
  node_size = 2,
  base_plot = NULL
)

Arguments

proj	object of class pm_project.
eccentricity	eccentricity of ellipses, defined as half the distance between foci divided by the semi-major axis. e = sqrt{1 - b^2/a^2}, where e is the eccentricity, a is the length of the semi-major axis, and b is the length of the semi-minor axis. Eccentricity ranges between 0 (perfect circle) and 1 (straight line between foci).
n	number of points that make up each ellipse.
alpha	the opacity of ellipses.
col_scale	the colour scale to use.
zlim	the limits of the colour scale. If NULL then these limits are chosen automatically.
node_size	the plotted size of nodes.
base_plot	optional base plot (object of class ggplot) on which this function builds. If NULL then a simple empty plot is used.

mrc-ide/PlasmoMAPI documentation built on Oct. 1, 2020, 9:41 a.m.