R/write_phyloseq.R

In microbiome: Microbiome Analytics

#' @title Exporting phyloseq Data in CSV Files
#' @description Writes the otu, taxonomy and metadata in csv files.
#' @param x \code{\link{phyloseq-class}} object
#' @param type 'OTU' or 'TAXONOMY' or 'METADATA'
#' @param path Path to the directory/folder where the data will be written.
#' Uses the working directory by default.
#' @return  Output file path (a string)
#' @seealso read_phyloseq
#' @export
#' @examples 
#' #data(dietswap)
#' #pseq <- dietswap
#' ## By default writes all info at once (ie OTU/TAXONOMY/METADATA)
#' #write_phyloseq(pseq) 
#' #write_phyloseq(pseq, 'OTU')
#' #write_phyloseq(pseq, 'TAXONOMY')
#' #write_phyloseq(pseq, 'METADATA')
#' @keywords utilities
write_phyloseq <- function(x, type="all", path=getwd()) {

    .Deprecated("", "The microbiome::write_phyloseq will be 
    deprecated in a future release.")

    type <- toupper(type)

    # TODO make read_phyloseq as well
    if (type == "OTU" || type == "all") {
        f <- paste(path, "otu_table.csv", sep="/")
        message("Writing OTU in the file ", f)
        # y <- as.data.frame(x@otu_table);
        if (f %in% dir(path)) {
            warning(paste("The file with the same name", f,
            "exists in the given path and is overwritten."))
        }
        # Let us use abundances function here as it is guaranteed to be taxa x
        # samples always
        y <- abundances(x)
        write.csv(y, file=f, fileEncoding="UTF-16LE")

    }

    if (type == "TAXONOMY" || type == "all") {
        # Renamed from TAXA to TAXONOMY as the latter is used elsewhere
        f <- paste(path, "taxonomy_table.csv", sep="/")
        message("Writing TAXONOMY in the file ", f)
        if (f %in% dir(path)) {
            warning(paste("The file with the same name", f,
            "exists in the given path and is overwritten."))
        }
        y <- as.data.frame(tax_table(x))
        write.csv(y, file=f, fileEncoding="UTF-16LE")

    }
    
    if (type == "METADATA" || type == "all") {
        f <- paste(path, "metadata_table.csv", sep="/")
        message("Writing METADATA in the file ", f)
        if (f %in% dir(path)) {
            warning(paste("The file with the same name", f,
            "exists in the given path and is overwritten."))
        }
        y <- meta(x)
        write.csv(y, file=f, fileEncoding="UTF-16LE")
    }
    
    return(path)
    
}