microbiome_barplot: microbiome_barplot

In xvtyzn/nyankomicro: Useful Functions for Bacterial Composition Analysis

Description

Create a bacterial composition plot

Usage

microbiome_barplot(
  physeq,
  level = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  plot_category,
  plot_percent = 10,
  color_methods = c("abundance", "common", "manual"),
  manual_color_palette = NULL,
  threshold = "max",
  na_str = c("unidentified", "uncultured")
)

Arguments

physeq	phyloseq object
level	taxonomy level
plot_category	metadata category (expect a vector of strings containing categories)
plot_percent	threshold persent
color_methods	coloring methods
threshold	the way of calculating threshold values
na_str	taxa name to be Undetermined

Details

Create a bacterial composition plot using a specific threshold value.

Value

barplot of microbiome composition as ggplot2 object

xvtyzn/nyankomicro documentation built on Jan. 21, 2022, 8:17 p.m.