Create an alluvial plot via the full workflow wrapper

Runs the alluvial workflow end-to-end:

1. prepare_alluvial_data: aggregate ASV-level RA to tax_level and compute group means,

2. classify_taxa_patterns: assign abundance-pattern classes and create tax_color,

3. generate_alluvial_palette: generate a palette for tax_color (skipped if custom_palette is provided),

4. plot_alluvial: draw the plot.

Usage

create_alluvial_plot(
  data,
  tax_level,
  group_col,
  SampleID_col = "SampleID",
  groups = NULL,
  low_abundance_threshold = 0.01,
  palette_list = NULL,
  custom_palette = NULL,
  prepare_args = list(),
  classify_args = list(),
  palette_args = list(),
  plot_args = list(),
  return_all = FALSE
)

Arguments

data

Raw long-format data with ASV-level RA and taxonomy columns.

tax_level

Character string naming the taxonomy rank to plot (e.g. "Class", "Family").

group_col

Character string naming the grouping column used on the x-axis.

SampleID_col

Character string naming the sample ID column (default: "SampleID").

groups

Optional character vector restricting groups included. If NULL, all groups are used.

low_abundance_threshold

Numeric threshold passed to classify_taxa_patterns (default: 0.01).

palette_list

Optional vector of HCL palette names passed to generate_alluvial_palette.

custom_palette

Optional named palette mapping tax_color keys to colors. If provided, palette generation is skipped.

prepare_args

Named list of extra arguments passed to prepare_alluvial_data.

classify_args

Named list of extra arguments passed to classify_taxa_patterns.

palette_args

Named list of extra arguments passed to generate_alluvial_palette (only used if custom_palette is NULL).

plot_args

Named list of extra arguments passed to plot_alluvial.

return_all

Logical; if TRUE, returns a list with intermediate objects: data_prepared, data_classified, palette, plot.

Value

A ggplot object, or a named list if return_all = TRUE.

Details

Additional arguments are routed to the underlying functions via the *_args lists.

Examples

if (FALSE) { # \dontrun{
library(dplyr)

toy <- tibble::tibble(
  SampleID = c("S1","S1","S2","S2"),
  Group    = c("G1","G1","G1","G1"),
  Class    = c("A","B","A","C"),
  RA       = c(0.7, 0.3, 0.6, 0.4)
)

res <- create_alluvial_plot(
  data = toy,
  tax_level = "Class",
  group_col = "Group",
  prepare_args = list(complete_zero = TRUE, clean_taxonomy = FALSE),
  classify_args = list(detect_mixed_abundance = TRUE),
  plot_args = list(alpha = 0.7),
  return_all = TRUE
)

res$plot
} # }