R/phy_to_ldf.R

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

#' @title Convert phyloseq object to long data format
#' @description Faster alternative to psmelt function from \code{\link{phyloseq-class}} object.
#' @param x \code{\link{phyloseq-class}} object
#' @param 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 \code{\link{transform}} function.
#' @return A data frame in long format with appropriate transfomation if requested.
#' @import tidyr
#' @import dplyr
#' @importFrom tibble rownames_to_column
#' @import microbiome
#' @export
#' @examples \dontrun{
#'   # Example data
#'     library(microbiomeutilities)
#'     data("biogeogut")
#'     pseq <- biogeogut
#'     pseq_df <- phy_to_ldf(pseq, transform.counts = NULL)
#'
#'           }
#' @keywords utilities
phy_to_ldf = function(x, transform.counts)
{

  if (is.null(transform.counts)) {
    x <- x
  } else if (transform.counts == "log10") {
    x <- transform(x, "log10")
  } else if (transform.counts == "Z-OTU") {
    x <- transform(x, "Z", "OTU")
  } else if (transform.counts == "Z-Sample") {
    x <- transform(x, "Z", "Sample")
  } else if (transform.counts == "compositional") {
    x <- transform(x, "compositional", "OTU")
  } else {
    stop("Please provide appropriate transformation")
  }

  message("An additonal column Sam_rep with sample names is created for reference purpose")
  meta_df = data.frame(sample_data(x))
  meta_df$Sam_rep <- rownames(meta_df)
  tax_df = data.frame(tax_table(x)) %>%
    rownames_to_column("OTUID")
  otu_df = data.frame(otu_table(x),
                      check.names = FALSE) %>% rownames_to_column("OTUID")
  suppressWarnings(suppressMessages(otu_df %>% left_join(tax_df) %>% gather_("Sam_rep",
                                           "Abundance", setdiff(colnames(otu_df),
                                                                "OTUID")) %>% left_join(meta_df)))
}