ezviz {mbX}R Documentation

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
)

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.

Value

A ggplot object containing the visualization.

Examples


  # Example usage (ensure that 'inst/extdata' contains the appropriate files):
  microbiome_data <- system.file("extdata", "microbiome.csv", package = "mbX")
  metadata <- system.file("extdata", "metadata.csv", package = "mbX")
  plot_obj <- ezviz(microbiome_data, metadata, "genus", "sample_type", top_taxa = 20)
  print(plot_obj)



[Package mbX version 0.1.3 Index]