Autoplot for pairwise distance matrices

This function provides a convenient way to visualize pairwise distance matrices (e.g., Fst, IBS) as heatmaps using ggplot2. It supports both matrix and tidy tibble formats, and can optionally reorder rows/columns using either an explicit ordering vector or a function (e.g. hierarchical clustering).

Usage

# S3 method for class 'pairwise_matrix'
autoplot(object, order = NULL, ...)

# S3 method for class 'pairwise_tbl'
autoplot(object, order = NULL, ...)

Arguments

object

A square numeric matrix OR a data.frame/tibble with 3 columns: names1, names2, value (half-matrix representation).

order

Optional ordering specification. Can be:

• NULL (default): preserve the existing order.

• A character vector containing all row/column names in the desired order.

• A function taking the matrix as input and returning either:

  • an ordering vector of indices, or

  • an object with an order component (e.g. from stats::hclust()).

...

Additional arguments (not currently used). Included for compatibility with autoplot generic.

Value

A ggplot object.

Examples

example_gt <- load_example_gt("gen_tbl")

# With a pairwise matrix:
fst_dist <- example_gt %>%
  group_by(population) %>%
  pairwise_pop_fst(method = "Nei87", type = "pairwise")

autoplot(fst_dist)


# Explicit ordering
autoplot(
  fst_dist,
  order = rev(rownames(fst_dist))
)


# Hierarchical clustering
autoplot(
  fst_dist,
  order = function(x) {
    stats::hclust(stats::as.dist(x), method = "complete")
  }
)


# With a tidy tibble of distances:
fst_tidy <- example_gt %>%
  group_by(population) %>%
  pairwise_pop_fst(method = "Nei87", type = "tidy")

autoplot(fst_tidy)


autoplot(
  fst_tidy,
  order = function(x) {
    stats::hclust(stats::as.dist(x))
  }
)