R/dimred_pcoa.R

In compbiomed/animalcules: Interactive microbiome analysis toolkit

#' Dimensionality reduction through PCoA
#'
#' @param MAE A multi-assay experiment object
#' @param tax_level The taxon level used for organisms
#' @param color A condition to color data points by e.g. "AGE"
#' @param shape A condition to shape data points by e.g. "SEX"
#' @param axx Principle coordinate on the x-axis e.g. 1
#' @param axy Principle coordinate on the y-axis e.g. 2
#' @param axz Principle coordinate on the z-axis e.g. 2
#' @param method Method to use e.g. c("bray", "jaccard")
#' @return A list with a plotly object and summary table
#'
#' @examples
#' data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
#' toy_data <- readRDS(data_dir)
#' result <- dimred_pcoa(toy_data,
#'   tax_level = "genus",
#'   color = "AGE",
#'   shape = "DISEASE",
#'   axx = 1,
#'   axy = 2,
#'   method = "bray"
#' )
#' result$plot
#' result$table
#'
#' @rawNamespace import(ape, except = where)
#' @import dplyr
#' @import scales
#' @import plotly
#' @import magrittr
#' @import reshape2
#' @import MultiAssayExperiment
#'
#' @export
dimred_pcoa <- function(MAE,
    tax_level,
    color,
    shape = NULL,
    axx = 1,
    axy = 2,
    axz = NULL,
    method = c("bray", "jaccard")) {
    # Default variables
    method <- match.arg(method)
    
    # Extract data
    microbe <- MAE[["MicrobeGenetics"]]
    tax_table <- as.data.frame(rowData(microbe)) # organism x taxlev
    sam_table <- as.data.frame(colData(microbe)) # sample x condition
    counts_table <-
        as.data.frame(assays(microbe))[, rownames(sam_table)] #organism x sample
    
    # Sum counts by taxon level and return counts
    df <- counts_table %>%
        # Sum counts by taxon level
        upsample_counts(tax_table, tax_level) %>%
        # Fix constant/zero row
        {
            if (sum(base::rowSums(as.matrix(.)) == 0) > 0) {
                . <- .[-which(base::rowSums(as.matrix(.)) == 0), ]
            } else {
                .
            }
        } %>%
        # Transpose
        t()
    
    # Distance metrics
    if (method == "bray") {
        df.dist <- vegan::vegdist(df, method = "bray")
    } else if (method == "jaccard") {
        df.dist <- vegan::vegdist(df, method = "jaccard")
    }
    
    # PCoA
    df.apcoa <- ape::pcoa(df.dist)
    # Principle Coordinates
    df.pcoa <- df.apcoa$vectors
    # Importance
    df.imp <- df.apcoa$values
    
    # Merge in covariate information
    if (!is.null(shape)) {
        df.pcoa.m <-
            merge(df.pcoa, sam_table[, c(color, shape), drop = FALSE],
                by = 0, all = TRUE
            )
        
        # When shape is required
        # Bypass duplicate colnames if color == shape
        shape <- colnames(df.pcoa.m)[ncol(df.pcoa.m)]
        df.pcoa.m[[shape]] <- as.factor(df.pcoa.m[[shape]])
    } else {
        df.pcoa.m <- merge(df.pcoa,
            sam_table[, color, drop = FALSE],
            by = 0, all = TRUE
        )
        shape <- "shape" # Referenced by plotly later
        df.pcoa.m[[shape]] <- 1 # Constant results in omitting shape
    }
    
    # Plotly | Scatterplot
    if (is.null(axz)) {
        # 2D Plot
        p <- plot_ly(df.pcoa.m,
            x = as.formula(paste("~Axis.", axx, sep = "")),
            y = as.formula(paste("~Axis.", axy, sep = "")),
            mode = "markers",
            color = as.formula(paste("~", color, sep = "")),
            symbol = as.formula(paste("~", shape, sep = "")),
            type = "scatter",
            text = df.pcoa.m$Row.names,
            marker = list(size = 10)
        )
    } else {
        # 3D Plot
        p <- plot_ly(df.pcoa.m,
            x = as.formula(paste("~Axis.", axx, sep = "")),
            y = as.formula(paste("~Axis.", axy, sep = "")),
            z = as.formula(paste("~Axis.", axz, sep = "")),
            mode = "markers",
            color = as.formula(paste("~", color, sep = "")),
            symbol = as.formula(paste("~", shape, sep = "")),
            symbols = c(
                "circle",
                "square", "diamond", "cross",
                "square-open", "circle-open",
                "diamond-open", "x"
            ),
            type = "scatter3d",
            text = df.pcoa.m$Row.names,
            marker = list(size = 6)
        )
    }
    
    p$p <- NULL # To suppress a shiny warning
    
    # Formatting importance table
    df.imp <- df.imp[, c(1, 3, 5)]
    rownames(df.imp) <- paste("Axis", seq_len(nrow(df.imp)), sep = ".")
    colnames(df.imp) <- c(
        "Eigenvalue",
        "Variance Explained",
        "Cumulative Variance"
    )
    
    df.imp[, "Eigenvalue"] <- signif(df.imp[, "Eigenvalue"], 3)
    
    # Show variance as a percentage
    df.imp[, 2] <- scales::percent(as.numeric(df.imp[, 2]))
    df.imp[, 3] <- scales::percent(as.numeric(df.imp[, 3]))
    
    # Reorder
    df.imp <- as.data.frame(df.imp)
    df.imp$Axis <- rownames(df.imp)
    df.imp <- df.imp[, c(4, 1, 2, 3)]
    
    return(list(plot = p, table = df.imp))
}