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.

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.