z_diversity: Calculate Zeta Diversity

In pctax: Professional Comprehensive Omics Data Analysis

Calculate Zeta Diversity

Description

This function calculates Zeta diversity for each group in the provided otutab.

This function plots the Zeta diversity results obtained from the z_diversity function.

Usage

z_diversity(otutab, group_df = NULL, zetadiv_params = list())

## S3 method for class 'zeta_res'
plot(x, lm_model = c("exp", "pl")[1], ribbon = FALSE, text = TRUE, ...)

Arguments

otutab	A matrix or data frame containing OTU (Operational Taxonomic Unit) counts.
group_df	A data frame containing group information.
zetadiv_params	Additional parameters to be passed to the Zeta.decline.mc function from the zetadiv package.
x	Zeta diversity results obtained from z_diversity function.
lm_model	The linear model to be used for fitting ('exp' or 'pl').
ribbon	Logical, whether to add a ribbon to the plot for standard deviation.
text	Logical, whether to add R-squared and p-value text annotations.
...	Additional arguments to be passed to ggplot2 functions.

Value

zeta_res

A ggplot object.

Examples

if (requireNamespace("zetadiv")) {
  data(otutab, package = "pcutils")
  zeta_result <- z_diversity(otutab, metadata["Group"], zetadiv_params = list(sam = 10))
  plot(zeta_result, lm_model = "exp", text = TRUE)
}

pctax documentation built on May 29, 2024, 10:03 a.m.