Skip to contents

Plot Taxonomic Distance Heatmap

Source: R/plot_heatmap.R
plot_heatmap.Rd

Visualizes the pairwise taxonomic distance matrix as a colored heatmap using ggplot2. Species are ordered by hierarchical clustering so that taxonomically similar species appear adjacent.

Usage

plot_heatmap(
  tax_tree,
  label_size = 3,
  title = NULL,
  low_color = "white",
  high_color = "#B22222"
)

Arguments

tax_tree

A data frame representing the taxonomic hierarchy, as produced by build_tax_tree.

label_size

Numeric value controlling the size of species labels. Default is 3.

title

Optional character string for the plot title.

low_color

Color for the lowest distance (most similar). Default is "white".

high_color

Color for the highest distance (most distant). Default is "#B22222" (firebrick red).

Value

A ggplot object.

Details

The heatmap displays the full symmetric distance matrix computed by tax_distance_matrix. The diagonal (self-distance = 0) appears in the lowest color. Species are reordered using hierarchical clustering (UPGMA) to reveal taxonomic groupings visually.

See also

tax_distance_matrix, plot_taxonomic_tree

Examples

# \donttest{
tax <- build_tax_tree(
  species = c("sp1", "sp2", "sp3", "sp4"),
  Genus   = c("G1", "G1", "G2", "G2"),
  Family  = c("F1", "F1", "F1", "F2")
)
plot_heatmap(tax)

# }