R/preparePlot.R

In NKInstinct/gater: Interactive Cytometry Gating in R

#' Prepare Plot for Interactive Gating
#'
#' A helper function for gs_gate_interactive to prepare the click-able flow
#' plots from ggcyto. All params are pulled from the parent call to
#' gs_gate_interactive.
#'
#' @param gs The GatingSet to use.
#' @param filterId Name of the gate to be drawn.
#' @param sample Which sample within the GatingSet to use for the plot (gates
#'   will be applied to all samples).
#' @param dims List of X and (optionally) Y parameters to plot.
#' @param subset The parent gate from which to draw the current plot.
#' @param bins Passed to geom_hex; how fine resolution the plot should be.
#' @param coords Passed to coord_cartesian; list of length-2 specifying the plot
#'   dimensions.
#' @param regate Boolean; should the gs first be stripped of gates matching the
#'   filterId?
#' @param overlayGates List of filterIds to plot on top of the current plot.
#'
#' @return A ggplot object ready to pass into the shiny app.
#' @noRd
#'
preparePlot <- function(gs, sample, dims, subset, bins, useCoords, coords, overlayGates,
                        addGateType, addCoords, useBiex, x_max, x_wide, x_pos,
                        x_neg, y_max, y_wide, y_pos, y_neg){
    sample.gs <- gs[[sample]]
    if(length(dims) > 2){
        warning("gs_gate_interactive can only handle one or two dims.
                The first two dims will be used, the others discarded.")
    }
    if(length(dims) == 1){
        gg <- ggcyto::ggcyto(sample.gs, aes(!!dims[[1]]), subset = subset) +
            geom_density() + scale_x_continuous(expand = c(0,0)) +
            scale_y_continuous(expand = c(0,0)) + theme_flowGate
        if(useCoords){
            gg <- gg + coord_cartesian(xlim = c(coords[[1]], coords[[2]]))
        }
    } else {
        gg <- ggcyto::ggcyto(
            sample.gs, aes(!!dims[[1]], !!dims[[2]]), subset = subset) +
                geom_hex(bins = bins) + scale_x_continuous(expand = c(0,0)) +
                scale_y_continuous(expand = c(0,0)) + theme_flowGate
        if(useCoords){
            gg <- gg + coord_cartesian(xlim = c(coords[[1]], coords[[2]]),
                                       ylim = c(coords[[3]], coords[[4]]))
        }
    }
    if(!is.null(overlayGates)){
        gg <- gg + geom_gate(overlayGates)
    } 
  
    if(addGateType == "polygonGate"){
        if(!is.null(addCoords) & nrow(addCoords) > 1){
            gg <- gg + geom_path(
                data = addCoords, aes(.data$x, .data$y), inherit.aes = FALSE)
        }
    }else if(addGateType == "quadGate"){
        gg <- gg + ggplot2::geom_vline(xintercept = addCoords$X) +
            ggplot2::geom_hline(yintercept = addCoords$Y)
    }
    if(useBiex){
        suppressMessages(if(length(dims)==1){
            gg <- gg + ggcyto::scale_x_flowjo_biexp(
                maxValue = x_max, widthBasis = x_wide, pos = x_pos, neg = x_neg)
        } else{
            gg <- gg + ggcyto::scale_x_flowjo_biexp(
                maxValue = x_max, widthBasis = x_wide, pos=x_pos, neg=x_neg) +
                ggcyto::scale_y_flowjo_biexp(
                maxValue = y_max, widthBasis = y_wide, pos = y_pos, neg = y_neg)
        })
    }
    gg <- ggcyto::as.ggplot(gg)
    return(gg)
}


theme_flowGate <- theme_gray() + theme(
        strip.background = element_blank(),
        strip.text = element_blank())