Autoplots for gt_admix objects — autoplot_gt

For gt_admix, the following types of plots are available:

cv: the cross-validation error for each value of k
barplot a standard barplot of the admixture proportions

Usage

# S3 method for class 'gt_admix'
autoplot(object, type = c("cv", "barplot"), k = NULL, run = NULL, ...)

Arguments

object: an object of class gt_admixture
type: the type of plot (one of "cv", and "barplot")
k: the value of k to plot (for barplot type only) param repeat the repeat to plot (for barplot type only)
run: the run to plot (for barplot type only)
...: additional arguments to be passed to autoplot method for q_matrices autoplot_q_matrix(), used when type is barplot.

Value

a ggplot2 object

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.

This autoplot will automatically rearrange individuals according to their id and any grouping variables if an associated 'data' gen_tibble is provided. To avoid any automatic re-sorting of individuals, set arrange_by_group and arrange_by_indiv to FALSE. See autoplot.q_matrix for further details.

Examples

# Read example gt_admix object
admix_obj <-
  readRDS(system.file("extdata", "anolis", "anole_adm_k3.rds",
    package = "tidypopgen"
  ))
# Cross-validation plot
autoplot(admix_obj, type = "cv")


# Basic barplot
autoplot(admix_obj, k = 3, run = 1, type = "barplot")


# Barplot with individuals arranged by Q proportion
# (using additional arguments, see `autoplot.q_matrix` for details)
autoplot(admix_obj,
  k = 3, run = 1, type = "barplot", annotate_group = TRUE,
  arrange_by_group = TRUE, arrange_by_indiv = TRUE,
  reorder_within_groups = TRUE
)