R/dplot_across_ru.R

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

#' dplot_across_ru
#' 
#' barplot of DoOR responses of a set of odorant across all responding units in
#' DoOR
#' 
#' @param odorant character vecto, one or several InChIKeys
#' @param response_matrix DoOR response matrix, a DoOR response matrix as data
#'   source
#' @param odor_data data frame, contains the odorant information.
#' @param zero character, an InChIKey of the odorant that should be set to 0
#' @param tag character, the chemical identifier to plot as odorant name (one of
#'   colnames(odor))
#' @param limits numeric of length 2, if provided the ylim will range
#'   accordingly
#' @param base_size numeric, the base font size for the ggplot2 plot
#'   
#' @return a ggplot object
#' @export
#' @author Daniel Münch <\email{daniel.muench@@uni-konstanz.de}>
#' @aliases dplot_acrossReceptors dplot_across_ru
#' @examples
#' # load data
#' library(DoOR.data)
#' library(DoOR.functions)
#' data(odor)
#' 
#' # plot activation pattern of one or several odorants
#' dplot_across_ru(trans_id("123-92-2"), tag = "CAS")
#' dplot_across_ru(odor$InChIKey[4:10])
#' 

dplot_across_ru <- function(odorant,
                  response_matrix = door_default_values("door_response_matrix"),
                  odor_data = door_default_values("odor"),
                  zero = door_default_values("zero"),
                  tag  = "Name",
                  limits,
                  base_size = 12) {
  if (!requireNamespace("ggplot2", quietly = TRUE))
    stop(
      "ggplot2 is required for plotting, please install via 
       install.packages('ggplot2')",
      call. = FALSE
    )
  
  if (!is.null(zero))
    response_matrix <-
      as.data.frame(apply(response_matrix, 2, function(x)
        reset_sfr(x, x[zero])))
  
  odorant <- as.character(odorant)
  
  data <- response_matrix[odorant, ]
  data <- door_melt(as.data.frame(data), na.rm = TRUE)
  
  if (tag != "InChIKey")
    data$odorant <-
    odor_data[match(data$odorant, odor_data$InChIKey), tag]
  
  plot <-
    ggplot2::ggplot(data,
                    ggplot2::aes(
                      x = odorant,
                      y = value,
                      fill = odorant,
                      color = odorant
                    )) +
    ggplot2::geom_bar(stat = "identity",
                      position = "identity",
                      alpha = .6) +
    ggplot2::facet_wrap(~ dataset) +
    ggplot2::theme_minimal(base_size = base_size) +
    ggplot2::theme(
      panel.border = ggplot2::element_rect(fill = NA, color = "grey"),
      axis.ticks.x = ggplot2::element_blank(),
      axis.text.x = ggplot2::element_blank(),
      axis.title.x = ggplot2::element_blank()
    )
  
  if (!missing(limits))
    plot <- plot + ggplot2::coord_cartesian(ylim = limits)
  
  return(plot)
  
}