Type: Package
Title: A Comprehensive Microbiome Data Processing Pipeline
Version: 0.2.0
Depends: R (≥ 4.1.0)
Description: Provides tools for cleaning, processing, and preparing microbiome sequencing data (e.g., 16S rRNA) for downstream analysis. Supports CSV, TXT, and Excel file formats. The main function, ezclean(), automates microbiome data transformation, including format validation, transposition, numeric conversion, and metadata integration. It also handles taxonomic levels efficiently, resolves duplicated taxa entries, and outputs a well-structured, analysis-ready dataset. The companion functions ezstat() run statistical tests and summarize results, while ezviz() produces publication-ready visualizations.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tools, readxl, openxlsx, dplyr, tidyr, ggplot2, rstatix, tibble, FSA, multcompView
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-07-23 22:43:52 UTC; ugalab4
Maintainer: Utsav Lamichhane <utsav.lamichhane@gmail.com>
Author: Utsav Lamichhane [aut, cre]
Repository: CRAN
Date/Publication: 2025-07-23 23:00:02 UTC

Clean and Process Microbiome Data

Description

Processes microbiome and metadata files (e.g., 16S rRNA sequencing data) to produce an analysis-ready dataset. Supports CSV, TXT, and 'Excel' file formats. This function validates file formats, reads the data, and merges the datasets by the common column 'SampleID'. If a 'Taxonomy' column exists, the data are filtered to include only rows matching the provided taxonomic level.

Usage

ezclean(microbiome_data, metadata, level = "d")

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").

Value

A data frame containing the cleaned and merged dataset.

Examples

## Not run: 
  mb  <- system.file("extdata", "microbiome.csv", package = "mbX")
  md  <- system.file("extdata", "metadata.csv",   package = "mbX")
  if (nzchar(mb) && nzchar(md)) {
    cleaned_data <- ezclean(mb, md, "g")
    head(cleaned_data)
  } else {
    message("Sample data files not found.")
  }

## End(Not run)

Statistical Analysis and Visualization of Microbiome Data

Description

Performs Kruskal_Wallis tests, post_hoc Dunn comparisons, Compact Letter Display (CLD) summaries, and generates boxplots annotated with CLD letters for taxa abundances grouped by a chosen metadata variable.

Usage

ezstat(microbiome_data, metadata, level, selected_metadata)

Arguments

microbiome_data

Character; path to the microbiome abundance table (CSV, TSV, XLS, or XLSX).

metadata

Character; path to the sample metadata file (CSV, TXT, XLS, or XLSX).

level

Character; taxonomic rank to aggregate at (e.g. "genus", "g").

selected_metadata

Character; name of the categorical metadata column to group by.

Details

This function first calls ezclean to produce a cleaned, merged table of sample IDs, metadata, and taxa abundances at the requested taxonomic level. It then:

  1. Runs Kruskal_Wallis tests on each taxon and writes results with FDR_correction.

  2. Performs Dunns pairwise post_hoc tests (BH_adjusted) for taxa with KW p less than or equal to 0.05.

  3. Computes CLD letters for significantly different groups and writes a summary Excel.

  4. Generates high-resolution (900 dpi) boxplots annotated with CLD letters.

Value

Invisibly returns the data.frame of cleaned sample_taxa abundances used for all analyses.

Examples

## Not run: 
  mb  <- system.file("extdata", "microbiome.csv", package = "mbX")
  md  <- system.file("extdata", "metadata.csv",   package = "mbX")
  if (nzchar(mb) && nzchar(md)) {
    ezstat(mb, md, "genus", "Group")
  }

## End(Not run)

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
)

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.

Value

A ggplot object containing the visualization.

Examples


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)