In DanielSprockett/reltools: Microbiome Amplicon Analysis and Visualization

# load packages
require(phyloseq)
require(reltools)
require(ggplot2)

# import data
data(GlobalPatterns)

Now we'll test one of our new fucntions, add_lowest_rank()

ps <- add_lowest_rank(GlobalPatterns)
print(colnames(tax_table(ps)))

The function works as expected!

ps <- subset_samples(ps, SampleType %in% c("Feces", "Skin", "Tongue"))
plot_ordered_bar(ps, x = "SampleType", y = "Abundance", fill = "Phylum", title = "Body Sites")

DanielSprockett/reltools documentation built on May 5, 2019, 12:27 p.m.