autoplot for clumppling objects — autoplot.gt

An autoplot method to generate quick visualisations for gt_clumppling objects. Available types are:

'modes': all aligned modes in structure plots over a multipartite graph, where better alignment between the modes is indicated by the darker color of the edges connecting their structure plots, and the cost of optimal alignment is labelled on each edge.
'modes_within_K': A set of figures, one for each number of clusters, with all modes with the same number of clusters in structure plots in one figure.
'major_modes': the major modes of each K aligned in a series of structure plots.
'all_modes': all aligned modes in a series of structure plots.

# S3 method for class 'gt_clumppling'
autoplot(
  object,
  type = c("modes", "modes_within_k", "major_modes", "all_modes"),
  group = NULL,
  k = NULL,
  ...
)

Arguments

object: a gt_clumppling object
type: the type of plot, one of 'modes', 'modes_within_K', 'major_modes' or 'all_modes'.
group: a vector of membership to a-priori groups (e.g. populations). Note that individuals from the same group need to be adjacent to each other
k: the k value to be plotted if 'type' is 'modes_within_k'
...: not used at the moment

Value

a plot

Details

autoplot produces simple plots to quickly inspect an object. They are not customisable; we recommend that you use ggplot2 to produce publication ready plots.

If you would like to generate an annotated autoplot, ensure that all individuals from the same population are adjacent to one another in the Q-matrix or gt_admix object supplied to gt_clumppling. Autoplot 'group' argument requires that all individuals from the same group are adjacent.