deseq2_tree: Show the results of deseq2 on the phylogenetic tree

In xvtyzn/nyankomicro: Useful Functions for Bacterial Composition Analysis

Description

Show the results of deseq2 on the phylogenetic tree

Usage

deseq2_tree(
  physeq,
  deseq2_results,
  level = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  alpha = 0.05,
  sample_annotation = "Status",
  vis_domain = FALSE,
  colors = nyankocolors,
  tree_adjust = 1.2
)

Arguments

physeq	phyloseq object
deseq2_results	deseq2 results object
level	visualize taxonomy level
alpha	threshold of adjusted p-values
sample_annotation	sample metadata used for drawing
vis_domain	domain level
colors	color palette
tree_adjust	value for ggtree positioning.

Value

ggplot2 object

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