R/tsne.R

In markgene/yamatClassifier: Yet Another Methylation Array Toolkit: Classifier

# tSNE

#' Run tSNE in batch mode.
#'
#' @param x A matrix.
#' @param n An integer scalar. Default to 10.
#' @param ... Any arguments passed to \code{\link[RTsne]{RTsne}}.
#' @return A list of the returned value of \code{\link[RTsne]{RTsne}}.
#' @export
tsne <- function(x, n = 10, ...) {
  lapply(seq(n), function(i) {
    Rtsne::Rtsne(X = x, ...)
  })
}


#' Plot tSNE result.
#'
#' @param tsne_res The returned value of \code{\link[RTsne]{RTsne}},
#'   which is a list.
#' @param ... Any arguments passed to \code{\link[ggplot2]{aes}}
#' @return A \code{\link[ggplot2]{ggplot}} object.
#' @export
plot_tsne <- function(tsne_res, ...) {
  tsne_res$Y %>%
    as.data.frame() %>%
    ggplot2::ggplot(., ggplot2::aes(
      x = V1,
      y = V2,
      ...
    )) +
    ggplot2::geom_point() +
    ggplot2::labs(x = "", y = "", colour = "Phenotype") +
    ggplot2::theme_light() +
    ggplot2::theme(
      axis.text.x = ggplot2::element_blank(),
      axis.text.y = ggplot2::element_blank()) +
    ggplot2::scale_colour_brewer(palette = "Set2")
}


#' Plot multiple tSNE results.
#'
#' @param x A list of the returned value of \code{\link[RTsne]{RTsne}}
#'   which itself is a list.
#' @param pheno A character or factor vector.
#' @param ... Any arguments passed to \code{\link[ggplot2]{aes}}
#' @return A \code{\link[ggplot2]{ggplot}} object.
#' @export
multiplot_tsne <- function(x, pheno, ...) {
  lapply(
    seq(length(x)),
    function(i) {
      as.data.frame(x[[i]]$Y) %>%
        dplyr::mutate(name = i) %>%
        dplyr::mutate(pheno = pheno)
    }) %>%
    do.call(rbind, .) %>%
    ggplot2::ggplot(., ggplot2::aes(
      x = V1,
      y = V2,
      colour = pheno,
      ...
    )) +
    ggplot2::geom_point() +
    ggplot2::labs(x = "", y = "", colour = "Phenotype") +
    ggplot2::scale_colour_brewer(palette = "Set2") +
    ggplot2::facet_wrap(~name, scales = "free", ) +
    ggplot2::theme_light() +
    ggplot2::theme(
      axis.text.x = ggplot2::element_blank(),
      axis.text.y = ggplot2::element_blank(),
      strip.background = ggplot2::element_blank(),
      strip.text.x = ggplot2::element_blank()
      )
}


#' Diagnose multiple tSNE runs with coordinates plot.
#'
#' @param x A list of the returned value of \code{\link[RTsne]{RTsne}}
#'   which itself is a list.
#' @param pheno A character or factor vector.
#' @param ... Any arguments passed to \code{\link[ggplot2]{aes}}
#' @return A \code{\link[ggplot2]{ggplot}} object.
#' @export
diagnose_tsne.coord <- function(x, pheno, ...) {
  df <- lapply(
    seq(length(x)),
    function(i) {
      as.data.frame(x[[i]]$Y)
    }) %>%
    do.call(cbind, .)
  p2 <- rep(seq(length(x)), each = 2)
  p3 <- rep(c("X", "Y"), length(x))
  colnames(df) <- paste0(p2, p3)
  df$pheno <- pheno
  df$name <- rownames(df)
  # Plot
  df %>%
    tidyr::gather(key = "Coordinate", value = "Position", -pheno, -name) %>%
    ggplot2::ggplot(., ggplot2::aes(
      x = Coordinate,
      y = Position,
      colour = pheno,
      group = name,
      ...
    )) +
    ggplot2::geom_line() +
    ggplot2::labs(x = "", y = "Position", colour = "Phenotype") +
    ggplot2::scale_colour_brewer(palette = "Set2") +
    ggplot2::theme_light()
}


#' Diagnose multiple tSNE runs with the correlations of coordinates.
#'
#' @param x A list of the returned value of \code{\link[RTsne]{RTsne}}
#'   which itself is a list.
#' @param pheno A character or factor vector.
#' @param ... Any arguments passed to \code{\link[ggplot2]{aes}}
#' @return A \code{\link[ggplot2]{ggplot}} object.
#' @export
diagnose_tsne.cor <- function(x, pheno, ...) {
  df <- lapply(
    seq(length(x)),
    function(i) {
      as.data.frame(x[[i]]$Y)
    }) %>%
    do.call(cbind, .)
  p2 <- rep(seq(length(x)), each = 2)
  p3 <- rep(c("X", "Y"), length(x))
  colnames(df) <- paste0(p2, p3)
  correlogram(t(df), pheno)
}