stacked_bar_plots: Stacked Bar Plots Based on Relative Abundance Data

In CoreMicrobiomeR: Identification of Core Microbiome

Stacked Bar Plots Based on Relative Abundance Data

Description

This function generates stacked bar plots for visualizing the relative abundance data of different operational taxonomic units (OTUs) in various samples.

Usage

stacked_bar_plots(data, num_samples_per_plot)

Arguments

data	A data frame containing the relative abundance data for the OTUs. The first column should contain the OTU IDs, and the subsequent columns should represent samples.
num_samples_per_plot	The number of samples to be displayed in each stacked bar plot.

Value

A list of interactive stacked bar plots, one for each group of samples, showing the relative abundance of OTUs in the samples.

Examples

#To run input data
core_1 <- CoreMicrobiome(
 otu_table = demo_otu,
 tax_table = demo_tax,
 metadata_table = demo_md,
 filter_type = "occupancy_fun_filter", #Or "abundance_fun_filter", Or "combined_filter"
 percent = 0.5,
 method = "css",  # Or "srs", "rrarefy", "tmm", "tmmwsp", "rle", "upperquartile", "none"
 beta_diversity_method = "jaccard",
 top_percentage = 10  # Adjust the percentage as needed for core/non-core OTUs
)
#To run the stacked bar plots function
stacked_plots <- stacked_bar_plots(core_1$core_otus_relative_abundance, 10)
#To view the stacked bar plot
stacked_plots[[1]]

CoreMicrobiomeR documentation built on May 29, 2024, 6:39 a.m.