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Plot Abundance-Occupancy Curve and Display the Core Taxa

Source: R/plot_abundance_occupancy.R
plot_abundance_occupancy.Rd

Creates a scatter plot showing the relationship between mean relative abundance and occupancy (occurrence frequency) of taxa, with core taxa highlighted.

Usage

plot_abundance_occupancy(core_result, core_set = "elbow")

Arguments

core_result

A list object returned by identify_core, containing at minimum:

  • occupancy_abundance: A data frame with columns otu, otu_rel (mean relative abundance), and otu_occ (occupancy).

  • elbow_core: Character vector of OTU IDs identified as core using the "elbow" method.

  • increase_core: Character vector of OTU IDs identified as core using the "increase" method.

core_set

Character string specifying which core set to highlight. Must be either "elbow" or "increase" (Default elbow).

Value

A ggplot object showing the abundance-occupancy plot with core taxa highlighted in red and non-core taxa in grey. The x-axis shows log10-transformed mean abundance and the y-axis shows occupancy (0-1).

Details

The function creates a scatter plot where each point represents a taxon (i.e. ASV or OTU). Core taxa (as defined by the selected method) are shown in red, while non-core taxa are shown in grey. The plot uses a log10 scale for abundance to better visualize the full range of abundances typically found in microbiome data.

See also

plot_core_distribution() and identify_core()

Examples

library(BRCore)

data("switchgrass_core", package = "BRCore")

p <- plot_abundance_occupancy(
  core_result = switchgrass_core,
  core_set = "increase"
)
print(p)