plot.troppca: Plot the Tropical Principal Components with Data Projections

In HoujieWang/Rtropical: Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

Plot the Tropical Principal Components with Data Projections

Description

Visualize the second order tropical principle components in troppca as a tropical triangle with projections on a two-dimensional plot via tropical isometry.

Usage

## S3 method for class 'troppca'
plot(
  x,
  point_class = NULL,
  fw = FALSE,
  plot.tree = FALSE,
  leaf.names = NULL,
  ntopology = 6,
  ...
)

Arguments

x	a fitted troppca object.
point_class	a vector of labels of all points in the given data matrix. Not needed for unlabeled data. (default: NULL)
fw	a logical variable to determine if to add Fermat-Weber point of the data projection. (default: FALSE)
plot.tree	a logical value indicating if to plot tree topology (default: FALSE)
leaf.names	the name of the leaves of the first tree in the data set (default: NULL)
ntopology	a numeric value indicating the number of most frequent tree topology to plot (default: 6)
...	Not used. Other arguments to plot

Value

plot.troppca does not return anything other than the plot.

HoujieWang/Rtropical documentation built on May 18, 2022, 11:56 a.m.