R/Spatial_marker_expression.R

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

#' Plotting a gene of interest in selected cells on the spatial image.
#' @param sample_names Character vector containing the name of the sample.
#' @param bcs_merge Data frame containing imagerow, imagecol and barcode of the cells belonging to the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 10.
#' @param images_tibble Tbl-df containing the sample name, grob, height and width of the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 5.
#' @param matrix Data frame containing all the genes detected per cells. This data frame can be obtained by the scaling_parameters functions.
#' @param marker Character vector containing the name of a gene of interest.
#' @param GEX_barcode Character vector containing the GEX barcode of the cell of interest with the -1 at the end
#' @param title Character vector to name the plot.
#' @param threshold Number, to define the threshold. If threshold = No, plot of the module and if threshold is a number, plot show the cells above the threshold.
#' @param size Number, to define the size of the text, default = 15.
#' @return Returns a plot of the level of expression of a gene in cells.
#' @export
#' @examples
#' \dontrun{
#' GEX_BCR_barcode<-vgm_with_simulated_VDJ$VDJ$GEX_barcode
#' GEX_BCR_barcode<-paste0(GEX_BCR_barcode,"-1") #Add -1 at the end of each barcode
#' #Without expression threshold
#' Spatial_marker_expression(matrix=scaling_parameters[[9]],
#' marker="CD3E",bcs_merge=scaling_parameters[[10]],
#' images_tibble=scaling_parameters[[5]],
#' GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells",
#' threshold = "No")
#'
#' #With expression threshold
#' Spatial_marker_expression(matrix=scaling_parameters[[9]],
#' marker="CD3E",bcs_merge=scaling_parameters[[10]],
#' images_tibble=scaling_parameters[[5]],
#' GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells",
#' threshold = 5)
#' }

Spatial_marker_expression<-function(sample_names,bcs_merge,images_tibble,matrix,marker, GEX_barcode,title,threshold,size){

  if(missing(sample_names)) stop("Please provide sample_names input for this function")
  if(missing(images_tibble)) stop("Please provide images_tibble input for this function")
  if(missing(bcs_merge)) stop("Please provide bcs_merge input for this function")
  if(missing(matrix)) stop("Please provide matrix input for this function")
  if(missing(marker)) stop("Please provide marker input for this function")
  if(missing(GEX_barcode)) stop("Please provide GEX_barcode input for this function or checked that the barcodes contain the -1 at the end")
  if(missing(title)){
    title <- ""}
  if(missing(size)){
    size = 15
  }
  if (missing(threshold)){
    threshold = "No"
  }

  platypus.version <- "v3"

  imagecol <- NULL
  imagerow <- NULL
  grob <- NULL
  barcode <- NULL
  width <- NULL
  height <- NULL

  geom_spatial <-  function(mapping = NULL,
                            data = NULL,
                            stat = "identity",
                            position = "identity",
                            na.rm = FALSE,
                            show.legend = NA,
                            inherit.aes = FALSE,
                            ...) {

    GeomCustom <- ggplot2::ggproto(
      "GeomCustom",
      ggplot2::Geom,
      setup_data = function(self, data, params) {
        data <- ggplot2::ggproto_parent(ggplot2::Geom, self)$setup_data(data, params)
        data
      },

      draw_group = function(data, panel_scales, coord) {
        vp <- grid::viewport(x=data$x, y=data$y)
        g <- grid::editGrob(data$grob[[1]], vp=vp)
        #ggplot2:::ggname("geom_spatial", g)
      },

      required_aes = c("grob","x","y")

    )

    ggplot2::layer(
      geom = GeomCustom,
      mapping = mapping,
      data = data,
      stat = stat,
      position = position,
      show.legend = show.legend,
      inherit.aes = inherit.aes,
      params = list(na.rm = na.rm, ...)
    )
  }

  #bind bcs_merge with markers
  test<-dplyr::bind_cols(bcs_merge,data.table::as.data.table(matrix)[, marker, with=FALSE])
  #subset of bcs_merge containing only cell selected
  bcs_merge_subset<-list()
  for (i in 1:length(GEX_barcode)){
    a<-dplyr::filter(test, barcode == GEX_barcode[[i]])
    bcs_merge_subset<-rbind(bcs_merge_subset,a)
  }
  names(bcs_merge_subset)[13]<-"marker"
  #Without threshold
  if (threshold == "No"){
    #colors
    myPalette <- grDevices::colorRampPalette(rev(RColorBrewer::brewer.pal(11, "Spectral")))
    #plot
    p<-ggplot2::ggplot(bcs_merge_subset,ggplot2::aes(x=imagecol,y=imagerow,fill=marker)) +
      geom_spatial(data=images_tibble[1,], ggplot2::aes(grob=grob), x=0.5, y=0.5)+
      ggplot2::geom_point(shape = 21, colour = "black", size = 1.75, stroke = 0.5)+
      ggplot2::coord_cartesian(expand=FALSE)+
      ggplot2::scale_fill_gradientn(colours = myPalette(100))+
      ggplot2::xlim(0,max(bcs_merge %>%
                            dplyr::filter(sample ==sample_names[1]) %>%
                            dplyr::select(width)))+
      ggplot2::ylim(max(bcs_merge %>%
                          dplyr::filter(sample ==sample_names[1]) %>%
                          dplyr::select(height)),0)+
      ggplot2::xlab("") +
      ggplot2::ylab("") +
      ggplot2::ggtitle(sample_names[1],title)+
      ggplot2::theme(axis.text=ggplot2::element_text(size=size),
            axis.title=ggplot2::element_text(size=size))+
      ggplot2::labs(fill = marker)+
      ggplot2::theme_set(ggplot2::theme_bw(base_size = size))+
      ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
            panel.grid.minor = ggplot2::element_blank(),
            panel.background = ggplot2::element_blank(),
            axis.line = ggplot2::element_line(colour = "black"),
            axis.text = ggplot2::element_blank(),
            axis.ticks = ggplot2::element_blank())
  } else{
    #thresholding
    for (i in 1:length(bcs_merge_subset$barcode)){
      if (bcs_merge_subset$marker[[i]]>=threshold){
        bcs_merge_subset$threshold[[i]] = 1
      } else{
        bcs_merge_subset$threshold[[i]] = 0
      }
    }
    #Add the threshold column to dataframe
    bcs_merge_subset$threshold<-as.numeric(bcs_merge_subset$threshold)
    bcs_merge_subset<-dplyr::filter(bcs_merge_subset,threshold==1)
    #plot
    p<-ggplot2::ggplot(data = bcs_merge_subset, ggplot2::aes(x=imagecol,y=imagerow, fill = as.factor(threshold)))+
      geom_spatial(data=images_tibble[1,], ggplot2::aes(grob=grob), x=0.5, y=0.5)+
      ggplot2::geom_point(shape=21, colour = "black", size = 1.75, stroke = 0.5)+
      ggplot2::coord_cartesian(expand=FALSE)+
      ggplot2::scale_fill_discrete(guide = ggplot2::guide_legend(reverse=TRUE))+
      ggplot2::xlim(0,max(bcs_merge %>%
                            dplyr::filter(sample ==sample_names[1]) %>%
                            dplyr::select(width)))+
      ggplot2::ylim(max(bcs_merge %>%
                          dplyr::filter(sample ==sample_names[1]) %>%
                          dplyr::select(height)),0)+
      ggplot2::xlab("") +
      ggplot2::ylab("") +
      ggplot2::ggtitle(sample_names[1], title)+
      ggplot2::theme(axis.text=ggplot2::element_text(size=size),
            axis.title=ggplot2::element_text(size=size))+
      ggplot2::labs(fill = marker)+
      ggplot2::guides(fill = ggplot2::guide_legend(override.aes = list(size=3)))+
      ggplot2::theme_set(ggplot2::theme_bw(base_size = size))+
      ggplot2::theme(legend.key = ggplot2::element_rect(fill = "white"))+
      ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
            panel.grid.minor = ggplot2::element_blank(),
            panel.background = ggplot2::element_blank(),
            axis.line = ggplot2::element_line(colour = "black"),
            axis.text = ggplot2::element_blank(),
            axis.ticks = ggplot2::element_blank())
  }
  return(p)
}