R/fcs_plot.R

In rodrigarc/RepertoiR: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

#' Plot flow data from index sorted cells
#'
#' @param processed_fcs_list List generated using `fcs_processing()` containing two data.frames
#'
#' @return Returns a ggplot object with a traditional flow density plot with the sorted cells and the selected thresholds for the two probes used in fcs_processing().
#'
#' @import ggplot2
#' @importFrom scales trans_breaks trans_format math_format
#'
#' @examples
#' index_sort_data <- fcs_processing(
#'     folder_path = system.file("/extdata/fcs_index_sorting",
#'                                 package = "scifer"),
#'     compensation = TRUE, plate_wells = 96,
#'     probe1 = "Pre.F", probe2 = "Post.F",
#'     posvalue_probe1 = 600, posvalue_probe2 = 400
#' )
#'
#' fcs_plot_obj <- fcs_plot(index_sort_data)
#'
#' @export
fcs_plot <- function(processed_fcs_list = NULL) {
    if (is.null(processed_fcs_list)) {
        stop("Input data.frame is NULL/empty")
    } else if (!is(processed_fcs_list, "list")) {
        stop("Input is not a list object")
    } else if (length(processed_fcs_list) != 2) {
        stop("Input is not a list with length 2")
    } else if (any(!is(processed_fcs_list[[1]], "data.frame") |
        !is(processed_fcs_list[[2]], "data.frame"))) {
        stop("At least one of the objects inside the list is not a data.frame")
    } else {
        ## Extract values for plotting
        probe1 <- processed_fcs_list[["selected_probes"]][1, 1]
        probe2 <- processed_fcs_list[["selected_probes"]][2, 1]
        posvalue_probe1 <- processed_fcs_list[["selected_probes"]][1, 2]
        posvalue_probe2 <- processed_fcs_list[["selected_probes"]][2, 2]
        ## Create object to remove NOTE error
        .x <- NULL
        flow_plot_obj <- ggplot(processed_fcs_list[["processed_fcs"]],
                                aes(x = get(probe1), y = get(probe2))) +
            geom_point(size = .7, color = "grey40") +
            scale_x_log10(
                breaks = scales::trans_breaks("log10", function(x) 10^x),
                labels = scales::trans_format("log10",
                                              scales::math_format(10^.x))
            ) +
            scale_y_log10(
                breaks = scales::trans_breaks("log10", function(x) 10^x),
                labels = scales::trans_format("log10",
                                              scales::math_format(10^.x))
            ) +
            geom_vline(xintercept = posvalue_probe1) +
            geom_hline(yintercept = posvalue_probe2) +
            labs(x = probe1, y = probe2) +
            theme_bw() +
            theme(
                panel.grid.major = element_blank(),
                panel.grid.minor = element_blank(),
                panel.background = element_rect(colour = "black", size = 1),
                axis.text = element_text(size = 10, color = "black"),
                axis.title = element_text(size = 12)
            ) +
            geom_density2d(color = "black") +
            annotation_logticks()
    }
    return(flow_plot_obj)
}