phy_to_ldf {microbiomeutilities}R Documentation

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)

[Package microbiomeutilities version 0.99.02 Index]