R/dplot_response_matrix.R

In ropensci/DoOR.functions: Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome

#' dplot_response_matrix
#' 
#' plot DoOR responses as a point matrix
#' 
#' @param data a subset of e.g. door_response_matrix
#' @param odor_data data frame, contains the odorant information.
#' @param tag the chemical identfier to plot (one of colnames(odor))
#' @param colors the colors to use if negative values are supplied (range of 5 
#'   colors, 2 for negative values, 1 for 0 and 3 for positive values)
#' @param limits the limits of the scale, will be calculated if not set
#' @param bw logical, whether to plot b&w or colored
#' @param point logical, if \code{TRUE} a point matrix instead of a heatmap will
#'   be returned (the default if you supply only positive values)
#' @param base_size numeric, the base font size for the ggplot2 plot
#' @param flip logical, if TRUE the x and y axes will be flipped
#' @param fix logical, whether to fix the ratio of the tiles when plotting as a 
#'   heatmap
#'   
#' @return a dotplot if limits[1] >= 0  or a heatmap if limits[1] < 0
#' @export
#' @author Daniel Münch <\email{daniel.muench@@uni-konstanz.de}>
#' @aliases dplot_responseMatrix dplot_response_matrix
#' @examples
#' # load data
#' library(DoOR.data)
#' data(door_response_matrix)
#' 
#' # reset the spontaneous firing rate to 0
#' tmp <- reset_sfr(door_response_matrix, "SFR")
#' 
#' # plot heatmap / coloured tiles
#' dplot_response_matrix(tmp[10:50,], tag = "Name", 
#'  limits = range(tmp, na.rm = TRUE))
#' 
#' # plot dotplot
#' dplot_response_matrix(door_response_matrix[10:50,], tag = "Name",
#'                         limits = range(door_response_matrix, na.rm = TRUE))
#' 
dplot_response_matrix <- function(data,
                                  odor_data = door_default_values("odor"),
                                  tag    = door_default_values("tag"),
                                  colors = door_default_values("colors"),
                                  flip = FALSE,
                                  fix = TRUE,
                                  bw     = FALSE,
                                  point  = FALSE,
                                  limits,
                                  base_size = 12) {
  if (!requireNamespace("ggplot2", quietly = TRUE))
    stop(
      "ggplot2 is required for plotting, please install via 
       install.packages('ggplot2')",
      call. = FALSE
    )
  if (!requireNamespace("grid", quietly = TRUE))
    stop("grid is required for plotting, please install via 
          install.packages('grid')",
         call. = FALSE)
  
  data   <- as.data.frame(data)
  
  # define limits and map colors of the colorscale
  if(missing(limits))
    limits <- range(data, na.rm=TRUE)

  if (limits[1] < 0) {
    values <-
      door_norm(c(limits[1], limits[1] / 2, 0, limits[2] / 3, limits[2] / 1.5, 
                  limits[2]))
  } else {
    values <- door_norm(c(0, limits[2] / 3, limits[2] / 1.5, limits[2]))
    colors <- colors[3:6]
  }
  
  data   <- door_melt(data = data, na.rm = TRUE)

  if(tag != "InChIKey")
    data$odorant <- odor_data[match(data$odorant, odor_data$InChIKey),tag]

  if(bw == TRUE & point == FALSE) {
    bw <- FALSE
    message("Plotting black&white heatmaps does not work, ignoring 'bw = TRUE'")
  }

  if(bw == TRUE & point == TRUE) {
    bw <- FALSE
    message("Sorry, but we can't plot negative sized points, 
             ignoring 'bw = FALSE'.")
  }

  if(missing(point) & missing(bw) & limits[1] >= 0) {
    point <- TRUE
    bw    <- TRUE
    message("Only positive values, returning b&w point plot.")
  }

  if(flip == TRUE) {
    plot <- ggplot2::ggplot(data, ggplot2::aes(x = odorant, y = dataset))
  } else {
    plot <- ggplot2::ggplot(data, ggplot2::aes(y = odorant, x = dataset))
  }


  plot <- plot +
    ggplot2::theme_minimal(base_size = base_size) +
    ggplot2::theme(axis.text.x = ggplot2::element_text(angle = -90, hjust = 0, 
                                                       vjust = .5))

  if (bw == FALSE & point == FALSE)
    plot <-
    plot + ggplot2::scale_fill_gradientn(
      colours  = colors,
      space = "Lab",
      values = values,
      limits  = limits
    )
  if (bw == FALSE & point == TRUE)
    plot <-
    plot + ggplot2::scale_color_gradientn(
      colours  = colors,
      space = "Lab",
      values = values,
      limits  = limits
    )
  
  
  if (point == FALSE) {
    plot <- plot + ggplot2::geom_tile(ggplot2::aes(fill = value))
  } else {
    if (bw == FALSE) {
      if (limits[1] < 0) {
        plot <-
          plot + ggplot2::geom_point(ggplot2::aes(size = abs(value), 
                                                  color = value), alpha = .6)
      } else {
        plot <-
          plot + ggplot2::geom_point(ggplot2::aes(size = value, 
                                                  color = value), alpha = .6)
      }
    } else {
      if (limits[1] < 0) {
        stop("Sorry, but we can't plot negative sized points, please try again 
              with 'bw = FALSE'.")
      } else {
        plot <-
          plot + ggplot2::geom_point(ggplot2::aes(size = value), alpha = .6)
      }
    }
  }
  
  if (fix == TRUE)
    plot <- plot + ggplot2::coord_fixed()
  
  return(plot)
}