R/beta.R

In yanpd01/yyeasy: Easy Use R

#' beta
#'
#' compute some dists.
#' Plot the PCA PCoa NMDS.
#' @rdname beta
#'
#' @param otu otu table.
#' @param tree phylogene tree
#'
#' @return beta dist
#' @examples
#' data(its)
#' tree <- ape::rtree(nrow(its), rooted = TRUE, tip.label = rownames(its))
#' dists <- beta_dist(its, tree)
#' pcoa_plot(dists[[3]])
#' @export
beta_dist <- function(otu, tree) {
    suppressMessages(
        if (missing(tree)) {
            tmp_phy <-
                phyloseq::phyloseq(phyloseq::otu_table(otu, taxa_are_rows = TRUE))
        } else {
            tmp_phy <-
                phyloseq::phyloseq(
                    phyloseq::otu_table(otu, taxa_are_rows = TRUE),
                    phyloseq::phy_tree(tree)
                )
        }
    )
    tmp_dists1 <- list(
        Bray_Curtis = phyloseq::distance(tmp_phy, "bray"),
        Jaccard     = phyloseq::distance(tmp_phy, "jaccard", binary = TRUE)
    )
    if (missing(tree)) {
        return(tmp_dists1)
    }
    tmp_dists2 <- list(
        Unweighted_UniFrac = phyloseq::distance(tmp_phy, "uunifrac"),
        Weighted_UniFrac   = phyloseq::distance(tmp_phy, "wunifrac")
    )
    return(c(tmp_dists1, tmp_dists2))
}