phy_to_ldf: Convert 'phyloseq-class' object to long data format

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Convert phyloseq-class object to long data format

Description

An alternative to psmelt function from phyloseq-class object.

Usage

phy_to_ldf(x, transform.counts)

Arguments

x	phyloseq-class object
transform.counts	Data transform to be used in plotting (but not in sample/taxon ordering). The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'. See the transform function

Value

A data frame in long format with appropriate transfomation if requested

Examples

## Not run: 
# Example data
library(microbiomeutilities)
data("zackular2014")
pseq <- zackular2014
pseq_df <- phy_to_ldf(pseq, transform.counts = NULL)

## End(Not run)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.