prep_mdf: Prepare melted phyloseq object to map colors to

In KarstensLab/microshades: A custom color palette for improving data visualization

Prepare melted phyloseq object to map colors to

Description

This function agglomerates a phyloseq object at a specified level and transforms counts to relative abundance. This function also melts the phyloseq object into a melted data frame which is used to apply microshades colors and organization to.

Usage

prep_mdf(
  ps,
  subgroup_level = "Genus",
  as_relative_abundance = TRUE,
  remove_na = FALSE
)

Arguments

ps	phyloseq-class object
subgroup_level	string of smaller taxonomic group
as_relative_abundance	transform counts to relative abundance
remove_na	remove NA values during taxa agglomeration

Details

Notes:

• This normalizes the phyloseq object to relative abundance

• This agglomerates to the smaller taxonomic group subgroup_level

Value

data.frame, a melted phyloseq object from psmelt()

Examples

library(phyloseq)
library(speedyseq)
data(GlobalPatterns)

# Use defaults
mdf <- prep_mdf(GlobalPatterns)

# Subgroup as "Family"
mdf_fam <- prep_mdf(GlobalPatterns, subgroup_level = "Family")

KarstensLab/microshades documentation built on June 11, 2024, 11:41 a.m.