Convert phyloseq-class object to long data format

Source: R/phy_to_ldf.R

An alternative to psmelt function from phyloseq-class object.

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

if (FALSE) {
# Example data
library(microbiomeutilities)
data("zackular2014")
pseq <- zackular2014
pseq_df <- phy_to_ldf(pseq, transform.counts = NULL)
}