R/tsneAnalysis.R

In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

#' @title dotsne
#' @description tSNE analysis for metflowClass object.
#' @author Xiaotao Shen
#' \email{shenxt@@sioc.ac.cn}
#' @param object A metflowClass object.
#' @param slot Group of data.
#' @param dims The number of dimensions.
#' @param perplexity perplexity.
#' @param colour.index colour.index
#' @param verbose verbose
#' @return A ggplot object.

dotsne = function(object,
                  slot = c("QC", "Subject"),
                  dims = 2,
                  perplexity = 30,
                  colour.index = c("class", "group", "batch"),
                  verbose = TRUE) {
  
  colour.index <- match.arg(colour.index)
  if (class(object) != "metflowClass") {
    stop("Only the metflowClass is supported!\n")
  }
  
  if (length(object@ms1.data) != 1) {
    stop("Please align batches first.\n")
  }
  
  if (any(!slot %in% c("QC", "Subject"))) {
    stop("Slot can only be QC and Subject.\n")
  }
  
  tag <- getData(object = object, slot = "Tags")
  name <- dplyr::pull(.data = tag, name)
  
  data <- lapply(slot, function(x) {
    x <- getData(object = object, slot = x)
    if (is.null(x)) {
      return(x)
    }
    rownames(x) <- name
    as.data.frame(t(x))
  })
  
  remain_idx <- which(!unlist(lapply(data, is.null)))
  slot <- slot[remain_idx]
  data <- data[remain_idx]
  
  class <- mapply(function(x, y) {
    rep(y, nrow(x))
  },
  x = data,
  y = slot)
  
  class <- unlist(class)
  
  data <- do.call(rbind, data)
  
  if (sum(is.na(data)) != 0) {
    stop("Please impute MV first.\n")
  }
  
  sample_info <- object@sample.info %>%
    filter(., sample.name %in% rownames(data))
  
  sample_info <- sample_info$sample.name %>%
    match(., rownames(data)) %>%
    `[`(sample_info, ., )
  colour.index <- pull(sample_info, var = colour.index)
  # colour.index <- factor(colour.index)
  tsne_object <- Rtsne::Rtsne(
    X = as.matrix(data),
    dims = dims,
    perplexity = perplexity,
    verbose = verbose
  )
  
  Y <- tsne_object$Y
  Y <-
    data.frame(Y, "Class" = colou.index, stringsAsFactors = FALSE)
  
  plot <- ggplot(Y, aes(X1, X2, colour = Class)) +
    geom_point() +
    labs(x = "Dimension 1",
         y = "Dimension 2") +
    theme_bw() +
    scale_colour_manual(values = c("#E64B35FF", "#4DBBD5FF")) +
    theme(
      axis.title = element_text(size = 15),
      axis.text = element_text(size = 12),
      legend.title = element_text(size = 15),
      legend.text = element_text(size = 12),
      strip.background = element_rect(fill = "#0099B47F"),
      strip.text = element_text(color = "white", size = 15)
    )
  plot
}