R/DIscBIO-generic-plottSNE.R

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

#' @title tSNE map
#' @description Visualizing the k-means or model-based clusters using tSNE maps
#' @param object \code{DISCBIO} class object.
#' @importFrom graphics text
#' @return A plot of t-SNEs.
setGeneric("plottSNE", function(object) {
  standardGeneric("plottSNE")
})

#' @rdname plottSNE
#' @export
setMethod(
  "plottSNE",
  signature = "DISCBIO",
  definition = function(object) {
    # ======================================================================
    # Validating
    # ======================================================================
    ran_k <- length(object@tsne) > 0
    ran_m <- length(object@MBtsne) > 0
    if (ran_k) {
      part <- object@kmeans$kpart
      x <- object@tsne
    } else if (ran_m) {
      part <- object@MBclusters$clusterid
      x <- object@MBtsne
    } else {
      stop("run comptsne before plottSNE")
    }
    # ======================================================================
    # Plotting
    # ======================================================================
    col <- c("black", "blue", "green", "red", "yellow", "gray")
    LEN <- length(levels(factor(part)))
    plot(
      x,
      las = 1,
      xlab = "Dim 1",
      ylab = "Dim 2",
      pch = 20,
      cex = 1.5,
      col = "lightgrey"
    )
    for (i in seq_len(LEN)) {
      if (sum(part == i) > 0) {
        text(
          x[part == i, 1],
          x[part == i, 2],
          i,
          col = col[i],
          cex = .75,
          font = 4
        )
      }
    }
  }
)