count_and_plot_ancestry_matrices {CKMRpop}

Count up the number of different kinds of related pairs and make a plot

Description

This counts up all the different types of pairwise relationships and makes a plot (or multiple pages of them). For an example, see the Vignette: vignette("species_1_simulation", package = "CKMRpop").

Usage

count_and_plot_ancestry_matrices(
  Pairs,
  nrow = 6,
  ncol = 5,
  white_ball_size = 1
)

Arguments

Pairs

a tibble like that returned by compile_related_pairs().

nrow

the number of rows to plot per page

ncol

the number of columns to plot per page

white_ball_size

the size of the white dot plotted on top of the primary shared ancestors' cells.

Value

Returns a list with the following components:

• highly_summarised: a tibble reporting counts of different types of relationships with the columns:

  • dom_relat: The name of the dominant relationship (e.g. Si, PO, A, etc).

  • max_hit: The number of primary shared ancestors.

  • n: The number of occurrences of this type of relationship.

• dr_counts: A tibble with the counts of all the different, unique ancestry match matrices observed, with the following columns:

  • dom_relat: The dominant relationship type

  • dr_hits: list column with the number of primary shared ancestors in the upper and lower quadrants of the ancestry match matrix (values are repeated for symmetrical relationships).

  • max_hit: the number of primary shared ancestors.

  • anc_match_matrix: a list column of ancestry match matrices.

  • n: The number of pairs with this type of ancestry match matrix

  • tot_dom: The total number of pairs within the given dominant relationship category.

  • ID: A unique, properly sorting name for this category for placing a title on facets of plots of these ancestry match matrices.

• dr_plots: a list named by the dominant relationship. Each component is a ggplot object which is a plot of the ancestry match matrices, faceted by their ID's as given in dr_counts.

• anc_mat_counts: A tibble summarizing the counts of different ancestry match matrices without regard to dominant relationship type, etc. Rows are arranged in descending order of number of pairs observed with each ancestry match matrix. It has the columns:

  • anc_match_matrix: a list column of ancestry match matrices.

  • n: the number of such matrices observed.

• anc_mat_plots: a list of ggplot pages. These are plots faceted by ancestry match matrix of all ancestry match matrices observed, ordered by number of occurrences (as given in anc_mat_counts).