tidypopgen (version 0.4.3)

autoplot_gt_admix: Autoplots for gt_admix objects

Description

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 gt_admix
autoplot(object, type = c("cv", "barplot"), k = NULL, run = NULL, ...)

Value

a ggplot2 object

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.

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
)