R/mfuzz-ggplot.R

In JoWatson2011/R4JW: What the Package Does (One Line, Title Case)

#' Fuzy C-Means Clustering and Visualisation
#' @description  From Jamie Soul; adapted from jspaezp on GitHub
#' @param data a dataframe or matrix
#' @param clustering mFuzz output
#' @param centre logical; should cluster centers be plotted
#' @param sort.columns logical; should column names be replaced by numbered numbers
#'
#' @return list containing ggplot object and dataframe of clustering values
#' @importFrom tidyr gather
#' @importFrom dplyr mutate select contains
#' @importFrom ggplot2 ggplot aes geom_line facet_grid geom_hline labs ylab scale_colour_gradient
#' @importFrom rlang .data
#' @export
#'
mFuzz.ggplot <- function(data, clustering,
                         centre = F, sort.columns=T) {

  clusterindex <- clustering$cluster

  # data frame with Membership values
  memship <- clustering$membership
  colnames(memship) <- paste("membership",
                             seq_along(memship[1,]),
                             sep = (""))

  exp <-data

  # This chunk replaces col names by numbers if
  # more than 1 is character only
  # or when sort.columns is FALSE

  all.char.cols <- !grepl("\\d", colnames(exp))
  if ((sum(all.char.cols) > 1) | !sort.columns) {
    colnames(exp) <- seq_along(all.char.cols)
  }

  exp <- data.frame(exp ,
                    Identifier = rownames(data),
                    clusterindex, memship,
                    stringsAsFactors = F)

  # Transform data frame into a ggplot-compatible format
  exp <- exp %>%
    gather(sample,
           expression ,
           - .data$Identifier,
           - .data$clusterindex,
           - contains("membership")) %>%
    mutate(Time = gsub("(\\w*\\D+(?=([0-9]+)))|((?<=\\d)\\D+$)",
                       "",
                       sample,
                       perl = TRUE)) %>%
    #  this regular expression deletes all characters and numbers prior to
    #  the last number in the string z.b. AA00AA00__00 -> 00 else keeps the string
    mutate(Time = gsub("^\\D*$", # this needs to be fixed, bug when seveal character cols ...
                       "0",
                       .data$Time,
                       perl = TRUE)) %>%
    mutate(Time = factor(.data$Time, ordered=T))

  exp$maxMembership <- exp %>%
    dplyr::select(contains("membership")) %>%
    apply(.data, 1, max)

  g <- ggplot(exp,
              aes(x = .data$Time, y = .data$expression)) +
    geom_line(
      aes(group = .data$Identifier,
          colour = .data$maxMembership)
    ) +
    scale_colour_gradient(low = "white", high = "red")

  # Center plotting when centre == TRUE
  if (centre) {
    centers <- clustering$centers %>%
      data.frame(.data,
                 clusterindex = rownames(.data),
                 stringsAsFactors = F) %>%
      gather(.data$sample,
             .data$Centre,
             - .data$clusterindex) %>%
      mutate(Time = gsub("(\\w*\\D+(?=([0-9]+)))|((?<=\\d)\\D+$)",
                         "",
                         sample,
                         perl = TRUE)) %>%
      #  this regular expression deletes all characters and numbers prior to
      #  the last number in the string z.b. AA00AA00__00 -> 00 else keeps the string
      mutate(Time = gsub("^\\D*$", # this needs to be fixed, bug when all character names
                         "0",
                         .data$Time,
                         perl = TRUE)) %>%
      mutate(Time = factor(.data$Time, ordered=T))
    g <- g + geom_line(data = centers, aes(x = .data$Time, y = .data$Centre))
  }

  g <- g + facet_grid(~ .data$clusterindex)
  g <- g + geom_hline(yintercept = 0,
                      colour="#666666", alpha = 0.5) +
    ylab("Fold change") + labs(fill= "Membership")

  return(list(g=g,exp=exp))
}