Plot Core Taxa Occupancy Across Metadata Groups

Creates a plot showing core taxa (i.e. OTUs/ASVs) occupancy patterns across a grouping variable.

Usage

plot_core_distribution(
  core_result,
  core_set = "elbow",
  group_var = "Crop",
  plot_type = c("bar", "line", "heatmap")
)

Arguments

core_result

A list object returned by identify_core, containing at minimum:

• otu_table: A data frame with ASV/OTUs as rows and samples as columns.

• metadata: A data frame with samples as rows and grouping variables as columns.

• otu_ranked: A data frame with ranked taxa containing:

  • otu: A column with taxa names.

  • rank: A column with the rank for each taxon.

• 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

Which core set to plot: "elbow" (default) or "increase".

group_var

Metadata column for bar coloring. Default: "sampling_date".

plot_type

Allows selection of 3 different plot types: bar, line, or heatmap.

Value

A ggplot2 object that can be further customized.

See also

identify_core(), plot_abundance_occupancy(), and plot_identified_core()

Examples

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

p <- plot_core_distribution(
  core_result = switchgrass_core,
  core_set = "increase",
  group_var = "sampling_date",
  plot_type = "bar"
)
print(p)