R/gs_gate_interactive.R

In NKInstinct/flowGate: Interactive Cytometry Gating in R

#' Interactive Manual Gating
#'
#' \code{gs_gate_interactive} opens a new graphical window where you can draw
#' rectangle, polygon, 1-D span, or 2-D quadrant gates that will be applied to
#' an entire GateSet (see the flowWorkspace package for complete information
#' about GateSets).
#'
#' @param gs The GateSet that will be gated on.
#' @param filterId String that gives the name of the new gate. Must be unique
#'   (can specify parent gates to aid in this).
#' @param sample Numeric specifying which of the GatingHierarchy objects (i.e.
#'   which FCS file/flow sample) that make up the GateSet do you want to use to
#'   draw the gate? Note that the gate you draw will be applied to all
#'   GatingHierarchy objects in the GateSet. Defaults to the first
#'   GatingHierarchy object in the GateSet.
#' @param dims A list of strings, length-1 or length-2, that specifies the x-
#'   and y- parameters that you will be gating on. Giving a length-1 list will
#'   result in a histogram, while a length-2 list will result in a dot-plot.
#'   Giving a length-3 or longer list will result in only the first two
#'   dimensions being used, and will generate a warning to say as much. Defaults
#'   to forward scatter ("FSC-A") and side scatter ("SSC-A").
#' @param subset String that gives the name of the parent gate that you want to
#'   sample from. For example, if you wanted to gate all live cells out of a
#'   previously drawn "lymphocytes" gate, you would specify "lymphocytes" here.
#'   Defaults to "root" (ungated).
#' @param regate A boolean specifying whether all gates with a name matching
#'   \code{filterId} should first be deleted before being re-drawn. Attempting
#'   to draw a gate with a non-unique \code{filterId} without specifying
#'   \code{regate = TRUE} will result in an error. Defaults to \code{FALSE}
#' @param overlayGates List of strings giving the \code{filterId}s of other
#'   gates to draw on the example plot when gating. Useful for drawing multiple
#'   gates on the same population (for example, after specifying a marker-low
#'   population, you can overlay the marker-low gate to aid in drawing a
#'   marker-high gate). Defaults to \code{NULL} (no overlaid gates).
#'
#' @examples
#'
#' path_to_fcs <- system.file("extdata", package = "flowGate")
#' fs <- read.flowSet(path = path_to_fcs,
#'                    pattern = ".FCS$",
#'                    full.names = TRUE)
#' gs <- GatingSet(fs)
#'
#' if(interactive()) { # only run in interactive sessions
#' gs_gate_interactive(gs,
#'                     filterId = "Lymphocytes",
#'                     dims = list("FSC-H", "SSC-H"))
#' }
#'
#' # returns gs with the same "Lymphocytes" gate on FSC-H and SSC-H applied to
#' # the root node (all events) of each sample in the GateSet.
#'
#' if(interactive()) {
#' gs_gate_interactive(gs,
#'                     filterId = "Live cells",
#'                     dims = "Viability",
#'                     subset = "Lymphocytes")
#' }
#'
#' # returns gs with a "Live cells" gate drawn on all cells included in the
#' # parent "Lymphocytes" gate. This gate would be based on a histogram of a
#' # marker called Viability, using the first GatingHierarchy sample as an
#' # example.
#'
#' if(interactive()){
#' gs_gate_interactive(gs,
#'                     filterId = "Live cells",
#'                     dims = list("Viability", "SSC-A"),
#'                     subset = "Lymphocytes",
#'                     regate = TRUE)
#' }
#'
#' # first deletes the "Live cells" gate drawn above, then adds a new "Live
#' # cells" gate to the set, this time based on a dot plot of Viability by
#' # side-scatter.
#'
#' if(interactive()){
#' gs_gate_interactive(gs,
#'                     filterId = "Dead cells",
#'                     dims = list("Viability", "SSC-A"),
#'                     subset = "Lymphocytes",
#'                     overlayGates = "Live cells")
#' }
#'
#' # returns gs with a "Dead cells" gate drawn on the same example graph that
#' # was used to draw the "Live cells" gate above. Overlays the "Live cells"
#' # gate on top of this graph to aid in drawing the "Dead cells" gate.
#'
#' @return A list of the interactively-specified parameters, including the drawn
#'   gate's coordinates, plot bins, and any flowjo biex coefs used to calculate
#'   those transforms.
#'
#' @import flowWorkspace
#' @import ggcyto
#' @import BiocManager
#' @importFrom ggplot2 aes_ aes geom_density scale_x_continuous
#' @importFrom ggplot2 scale_y_continuous geom_path geom_hex
#' @importFrom ggplot2 theme element_blank coord_cartesian
#' @importFrom rlang .data
#' @importFrom shiny updateTabsetPanel reactive
#'
#' @export
gs_gate_interactive <- function(
    gs, filterId, sample = 1, dims = list("FSC-A", "SSC-A"), subset = "root", 
    regate = FALSE, overlayGates = NULL){
    # Delete gate if regating ==================================================
    if(regate == TRUE){gs_pop_remove(gs, filterId)}
    # Server Function ==========================================================
    server <- function(input, output, session) {
        vals <- shiny::reactiveValues(gateCoords = data.frame(
            "x" = numeric(), "y" = numeric()))
        # Biex Handling --------------------------------------------------------
        shiny::observeEvent(input$useBiex, {
            if(input$useBiex){
                updateTabsetPanel(inputId = "biexTab", selected = "biexPanel")
            }else{
                updateTabsetPanel(inputId = "biexTab", selected = "blankPanel")
            }})
        transX <- reactive(flowjo_biexp(
            maxValue = input$xMaxVal, pos = input$xPos, neg = input$xNeg,
            widthBasis = input$xWidth, inverse = TRUE))
        transY <- reactive(flowjo_biexp(
            maxValue = input$yMaxVal, pos = input$yPos, neg = input$yNeg,
            widthBasis = input$yWidth, inverse = TRUE))
        # Prepare main panel plot ----------------------------------------------
        FPlot <- reactive(preparePlot(
            gs, sample, dims, subset, input$bins, input$useCoords, 
            c(input$XMin, input$XMax, input$YMin, input$YMax), overlayGates, 
            input$gateType, vals$gateCoords, input$useBiex, input$xMaxVal, 
            input$xWidth, input$xPos, input$xNeg, input$yMaxVal, input$yWidth,
            input$yPos, input$yNeg))
        output$plot1 <- shiny::renderPlot(FPlot(), height = function() {
            session$clientData$output_plot1_width})
        output$filterId <- shiny::renderText({paste0("Gate Name: ", filterId)})
        output$subset <- shiny::renderText({paste0("subset of: ", subset)})
        # Gate Handling --------------------------------------------------------
        gateH <- reactive(gateHandler(
            input$gateType, input$plot1_brush, input$plot1_click, input$useBiex,
            transX(), transY(), vals$gateCoords))
        shiny::observeEvent(input$plot1_brush, {vals$gateCoords <- gateH()})
        shiny::observeEvent(input$plot1_click, {vals$gateCoords <- gateH()})
        shiny::observeEvent(input$reset, {
            vals$gateCoords <- data.frame("x" = numeric(), "y" = numeric())})
        # Apply gate and close -------------------------------------------------
        shiny::observeEvent(input$done, {
            output <- applyGateClose(
                gs, subset, vals$gateCoords, input$gateType, filterId, FPlot(), 
                input$useBiex, input$bins, input$xMaxVal, input$xWidth, 
                input$xPos, input$xNeg, input$yMaxVal, input$yWidth, input$yPos, 
                input$yNeg)
            shiny::stopApp(output)})}
    shiny::runApp(shiny::shinyApp(ui, server))
}