Bubble Chart of Species Contributions to Diversity

Creates a bubble chart showing each species' abundance (x-axis), average taxonomic distance to other species (y-axis), and relative contribution to the community (bubble size). Species that are both abundant and taxonomically distant from others contribute most to overall taxonomic diversity.

Usage

plot_bubble(community, tax_tree, color_by = NULL, title = NULL)

Arguments

community: Named numeric vector of species abundances.
tax_tree: A data frame representing the taxonomic hierarchy, as produced by build_tax_tree.
color_by: Character string specifying which taxonomic rank to use for coloring bubbles. Must match a column name in tax_tree. If NULL (default), the highest available rank is used.
title: Optional character string for the plot title.

Value

A ggplot object.

Details

For each species $i$, the average taxonomic distance is calculated as:

$$\bar{\omega}_i = \frac{1}{S-1} \sum_{j \neq i} \omega_{ij}$$

where $\omega_{ij}$ is the pairwise taxonomic distance and $S$ is the number of species. Bubble size represents the product of relative abundance and average distance, indicating each species' contribution to overall taxonomic diversity.

Examples

# \donttest{
comm <- c(sp1 = 25, sp2 = 18, sp3 = 30, sp4 = 12, sp5 = 8)
tax <- build_tax_tree(
  species = paste0("sp", 1:5),
  Genus   = c("G1", "G1", "G2", "G2", "G3"),
  Family  = c("F1", "F1", "F1", "F2", "F2"),
  Order   = c("O1", "O1", "O1", "O1", "O1")
)
plot_bubble(comm, tax)

# }