mbX (version 0.2.0)

ezviz: Visualize Microbiome Data

Description

Generates publication-ready visualizations for microbiome data. This function first processes the microbiome and metadata files using ezclean(), then creates a bar plot using ggplot2. Supported file formats are CSV, TXT, and 'Excel'. Note: Only one of the parameters top_taxa or threshold should be provided.

Usage

ezviz(
  microbiome_data,
  metadata,
  level,
  selected_metadata,
  top_taxa = NULL,
  threshold = NULL,
  flip = FALSE
)

Value

A ggplot object containing the visualization.

Arguments

microbiome_data

A string specifying the path to the microbiome data file.

metadata

A string specifying the path to the metadata file.

level

A string indicating the taxonomic level for filtering the data (e.g., "genus").

selected_metadata

A string specifying the metadata column used for grouping.

top_taxa

An optional numeric value indicating the number of top taxa to keep. Use this OR threshold, but not both.

threshold

An optional numeric value indicating the minimum threshold value; taxa below this threshold will be grouped into an "Other" category.

flip

Logical. If `TRUE`, the order of the stacks is reversed.

Examples

# \donttest{
mb  <- system.file("extdata", "microbiome.csv", package = "mbX")
md  <- system.file("extdata", "metadata.csv",   package = "mbX")
plot_obj <- ezviz(
  microbiome_data = mb,
  metadata        = md,
  level           = "genus",
  selected_metadata    = "sample_type",
  top_taxa        = 20,
  flip            = FALSE
)
print(plot_obj)
# }