plot_stacked_bar: plot_stacked_bar

In yeguanhuav/visualization416S: Visualization functions for 16S and Metagenomics analysis

plot_stacked_bar

Description

This is a function for stacked barplot. PS: When faceting the stacked bar plot, use facet_wrap( vars(column_name), scales = "free_x")

Usage

plot_stacked_bar(
  phyloseq = NULL,
  level = NA,
  feature = NA,
  otu_table = NULL,
  metadata = NULL,
  order = NULL,
  relative_abundance = TRUE,
  legend_position = "top",
  colors = NULL,
  collapse = 0.01,
  title = NA,
  x_text_angle = 90
)

Arguments

phyloseq	A phyloseq object contain otu table, taxonomy table, sample metadata and phylogenetic tree. Set it to NULL if using an OTU table and metadata to draw the stacked barplot.
level	A taxonomy level to plot stacked bar. Default is NA. Required when using phyloseq object.
feature	The feature that will show as a colorbar under x axis. Default is NA.
otu_table	An OTU table. Taxa are colnames, SampleID are rownames (just like phyloseq). Set it to NULL if using phyloseq.
metadata	A metadata for the OTU table. SampleID are rownames (just like phyloseq). Set it to NULL if using phyloseq.
order	A vector of arranged SampleID in wanted order. Default is NULL. If NULL, plot_stacked_bar will automatically arrange samples by the most abundance taxonomy in decreasing order.
relative_abundance	Turn plot into relative abundance or not. Default is TRUE.
legend_position	Legend position. Default is "top". legend_position should be one of "none", "left", "right", "bottom", "top".
colors	A vector of colors. The number of colors should be larger than the number of level. Default is NULL, if NULL, plot_stacked_bar will use distinctive_colors for the plot.
collapse	Default is 0.01, collapse taxonomy which abundance is lower than 1 percent of total into "Others". Set it to FALSE if want to show all taxonomy levels.
title	Default is NA, value for ggplot2::labs(title).
x_text_angle	Default is 90, value for ggplot2::ggplot(themt(axis.text.x = element_text( angle))).

Examples

# Minimum usage
plot_stacked_bar(demo_phyloseq_object, level = "Genus")

yeguanhuav/visualization416S documentation built on March 22, 2022, 9:03 p.m.