R/abundances-methods.R

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

# This function is inspired from microbiome::abundances

#' Extract taxa abundances
#'
#' Extract taxa abundances from phyloseq objects.
#'
#' @param object [`otu_table-class`], [`phyloseq-class`], or
#'   [`microbiomeMarker-class`].
#' @param transform transformation to apply, the options inclulde:
#' * "identity", return the original data without any transformation.
#' * "log10", the transformation is `log10(object)`, and if the data contains
#'   zeros the transformation is `log10(1 + object)`.
#' * "log10p", the transformation is `log10(1 + object)`.
#' @param norm logical, indicating whether or not to return the normalized
#'   taxa abundances.
#' @return abundance matrix with taxa in rows and samples in columns.
#' @seealso [`otu_table-class`], [`phyloseq-class`],
#' [`microbiomeMarker-class`],[`transform_abundances`]
#' @docType methods
#' @rdname abundances-methods
#' @export
#' @examples
#' data(caporaso)
#' abd <- abundances(caporaso)
setGeneric(
    "abundances",
    function(object,
    transform = c("identity", "log10", "log10p"),
    norm = FALSE) {
        standardGeneric("abundances")
    }
)

# otu_table object
#' @aliases abundances, otu_table-method
#' @rdname abundances-methods
setMethod(
    abundances, "otu_table",
    function(object, 
        transform = c("identity", "log10", "log10p"),
        norm = FALSE) {
        transform <- match.arg(transform, c("identity", "log10", "log10p"))
        obj_transed <- transform_abundances(object, transform = transform)
        abd <- as(otu_table(obj_transed), "matrix")

        if (norm) {
            nf <- get_norm_factors(object)
            if (!is.null(nf)) {
                abd <- sweep(abd, 2, nf, "/")
            }
        }

        abd
    }
)

# phyloseq object
#' @aliases abundances,phyloseq-method
#' @rdname abundances-methods
setMethod(
    abundances, "phyloseq",
    function(object,
        transform = c("identity", "log10", "log10p"),
        norm = FALSE) {
        transform <- match.arg(transform, c("identity", "log10", "log10p"))
        otu <- otu_table(object)
        if (norm) {
            nf <- get_norm_factors(object)
            if (!is.null(nf)) {
                attr(otu, "norm_factor") <- nf
            }
        }
        otu <- abundances(otu, transform = transform, norm = norm)

        otu
    }
)

# microbiomeMarker object
#' @aliases abundances,microbiomeMarker-method
#' @rdname abundances-methods
setMethod(
    abundances, "microbiomeMarker",
    function(object,
        transform = c("identity", "log10", "log10p")) {
        transform <- match.arg(transform, c("identity", "log10", "log10p"))
        otu <- otu_table(object)
        otu <- abundances(otu, transform = transform, norm = FALSE)

        otu
    }
)