R/cyto_plot_gate-methods.R

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

#' Plot Gate Objects onto an Existing Plot
#'
#' @param x gate object of class
#'   \code{\link[flowCore:rectangleGate-class]{rectangleGate}},
#'   \code{\link[flowCore:polygonGate-class]{polygonGate}},
#'   \code{\link[flowCore:ellipsoidGate-class]{ellipsoidGate}}, \code{list} or
#'   \code{\link[flowCore:filters-class]{filters}}.
#' @param ... additional method-specific arguments.
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @seealso \code{\link{cyto_plot_gate,rectangleGate-method}}
#' @seealso \code{\link{cyto_plot_gate,polygonGate-method}}
#' @seealso \code{\link{cyto_plot_gate,ellipsoidGate-method}}
#' @seealso \code{\link{cyto_plot_gate,list-method}}
#' @seealso \code{\link{cyto_plot_gate,filters-method}}
#'
#' @export
setGeneric(
  name = "cyto_plot_gate",
  def = function(x, ...) {
    standardGeneric("cyto_plot_gate")
  }
)

#' Plot rectangleGate Objects onto an Existing plot
#'
#' @param x an object of class
#'   \code{\link[flowCore:rectangleGate-class]{rectangleGate}}.
#' @param channels fluorescent channels to used to construct the plot.
#' @param gate_line_type integer [0,6] which controls the line type, set to
#'   \code{1} to draw solid lines by default.
#' @param gate_line_width numeric to adjust line thickness of gates, set to
#'   \code{2.5} by default.
#' @param gate_line_col indicates the colour of the gate to be constructed, set
#'   to \code{"red"} by default.
#' @param gate_point logical indicating whether points should be included when
#'   plotting the gates, set to \code{FALSE} by default.
#' @param gate_point_shape integer [0,25] passed to pch to control the shape of
#'   the points, set to \code{16} to draw filled circles by default. For other
#'   shapes refer to \code{\link[graphics:points]{?pch}}.
#' @param gate_point_size numeric character expansion to control the size of the
#'   points in the drawn gate, set to \code{1} by default.
#'
#' @return gate object with modified co-ordinates for plotting.
#'
#' @importFrom flowCore parameters
#' @importFrom graphics par rect lines abline points
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @seealso \code{\link{cyto_plot_gate,polygonGate-method}}
#' @seealso \code{\link{cyto_plot_gate,ellipsoidGate-method}}
#' @seealso \code{\link{cyto_plot_gate,list-method}}
#' @seealso \code{\link{cyto_plot_gate,filters-method}}
#'
#' @examples
#' library(CytoRSuiteData)
#' 
#' # Load in samples
#' fs <- Activation
#' gs <- GatingSet(fs)
#' 
#' # Apply compensation
#' gs <- compensate(gs, fs[[1]]@description$SPILL)
#' 
#' # Transform fluorescent channels
#' trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
#' gs <- transform(gs, trans)
#' 
#' # Gate using gate_draw
#' gating(Activation_gatingTemplate, gs)
#' 
#' # Plot
#' cyto_plot(gs[[4]],
#'   parent = "T Cells",
#'   channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
#'   axes_trans = trans
#' )
#' 
#' # CD4 T Cells gate
#' cyto_plot_gate(getGate(gs, "CD4 T Cells")[[1]],
#'   channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
#'   gate_line_col = "purple"
#' )
#' @export
setMethod(cyto_plot_gate,
  signature = "rectangleGate",
  definition = function(x,
                          channels,
                          gate_line_type = 1,
                          gate_line_width = 2.5,
                          gate_line_col = "red",
                          gate_point = FALSE,
                          gate_point_shape = 16,
                          gate_point_size = 1) {

    # Assign x to gt
    gt <- x

    # Allow 1D gate plotted in 2D
    if (!missing(channels)) {
      if (length(channels) == 2 & length(parameters(gt)) == 1) {
        rg <- matrix(c(
          as.numeric(gt@min),
          as.numeric(gt@max),
          -Inf, Inf
        ),
        ncol = 2,
        nrow = 2
        )
        colnames(rg) <- c(
          as.vector(parameters(gt)),
          channels[!channels == as.vector(parameters(gt))]
        )
        rownames(rg) <- c("min", "max")
        gt <- rectangleGate(.gate = rg)
      }
    } else {
      channels <- as.vector(parameters(gt))
    }

    # 2D gatre in 1D
    if (length(channels) == 1 & length(parameters(gt)) == 2) {
      gt <- gt[channels]
    }

    if (!all(as.vector(parameters(gt)) %in% channels)) {
      stop(paste(
        "Channels argument should contain",
        paste(parameters(gt), collapse = " & "),
        "to plot supplied gate(s)."
      ))
    }

    # 2D rectangleGate
    if (length(gt@min) == 2) {

      # Replace -Inf x values for plotting
      if (is.infinite(gt@min[channels[1]]) |
        gt@min[channels[1]] < (par("usr")[1] - 0.13 * par("usr")[1])) {
        gt@min[channels[1]] <- (par("usr")[1] - 0.13 * par("usr")[1])
      }

      # Replace Inf x values for plotting
      if (is.infinite(gt@max[channels[1]]) |
        gt@max[channels[1]] > 0.98 * par("usr")[2]) {
        gt@max[channels[1]] <- 0.98 * par("usr")[2]
      }

      # Replace -Inf y values for plotting
      if (is.infinite(gt@min[channels[2]]) |
        gt@min[channels[2]] < (par("usr")[3] - 0.13 * par("usr")[3])) {
        gt@min[channels[2]] <- (par("usr")[3] - 0.13 * par("usr")[3])
      }

      # Replace Inf y values for plotting
      if (is.infinite(gt@max[channels[2]]) |
        gt@max[channels[2]] > 0.98 * par("usr")[4]) {
        gt@max[channels[2]] <- 0.98 * par("usr")[4]
      }

      # Add points to gate
      if (gate_point == TRUE) {
        points(
          x = c(gt@min[channels[1]], gt@max[channels[1]]),
          y = c(gt@min[channels[2]], gt@max[channels[2]]),
          col = gate_line_col,
          pch = gate_point_shape,
          cex = gate_point_size
        )
      }

      rect(
        xleft = gt@min[channels[1]],
        ybottom = gt@min[channels[2]],
        xright = gt@max[channels[1]],
        ytop = gt@max[channels[2]],
        border = gate_line_col,
        lwd = gate_line_width,
        lty = gate_line_type
      )
    } else if (length(gt@min) == 1) {

      # Replace -Inf values for plotting
      if (is.infinite(gt@min[1]) |
        gt@min[1] < (par("usr")[1] - 0.13 * par("usr")[1])) {
        gt@min[1] <- (par("usr")[1] - 0.13 * par("usr")[1])
      }

      # Replace Inf values for plotting
      if (is.infinite(gt@max[1]) |
        gt@max[1] > 0.98 * par("usr")[2]) {
        gt@max[1] <- 0.98 * par("usr")[2]
      }

      # Add points (x1,hln) and (x2, hln)
      if (gate_point == TRUE) {
        points(
          x = c(
            gt@min[channels[1]], gt@min[channels[1]],
            gt@max[channels[1]], gt@max[channels[1]]
          ),
          y = c(
            gt@min[channels[2]], gt@min[channels[2]],
            gt@max[channels[2]], gt@max[channels[2]]
          ),
          col = gate_line_col,
          pch = gate_point_shape,
          cex = gate_point_size
        )
      }

      # Add rectangle
      rect(
        xleft = gt@min[channels[1]],
        ybottom = 0.6 * par("usr")[3],
        xright = gt@max[channels[1]],
        ytop = 0.985 * par("usr")[4],
        border = gate_line_col,
        lwd = gate_line_width,
        lty = gate_line_type
      )
    }

    invisible(gt)
  }
)

#' Plot polygonGate Objects onto an Existing Plot
#'
#' @param x an object of class
#'   \code{\link[flowCore:polygonGate-class]{polygonGate}}.
#' @param channels fluorescent channels to used to construct the plot.
#' @param gate_line_type integer [0,6] which controls the line type, set to
#'   \code{1} to draw solid lines by default.
#' @param gate_line_width numeric to adjust line thickness of gates, set to
#'   \code{2.5} by default.
#' @param gate_line_col indicates the colour of the gate to be constructed, set
#'   to \code{"red"} by default.
#' @param gate_point logical indicating whether points should be included when
#'   plotting the gates, set to \code{FALSE} by default.
#' @param gate_point_shape integer [0,25] passed to pch to control the shape of
#'   the points, set to \code{16} to draw filled circles by default. For other
#'   shapes refer to \code{\link[graphics:points]{?pch}}.
#' @param gate_point_size numeric character expansion to control the size of the
#'   points in the drawn gate, set to \code{1} by default.
#'
#' @return gate object with modified co-ordinates for plotting.
#'
#' @importFrom flowCore parameters
#' @importFrom graphics par points polygon
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @seealso \code{\link{cyto_plot_gate,rectangleGate-method}}
#' @seealso \code{\link{cyto_plot_gate,ellipsoidGate-method}}
#' @seealso \code{\link{cyto_plot_gate,list-method}}
#' @seealso \code{\link{cyto_plot_gate,filters-method}}
#'
#' @examples
#' library(CytoRSuiteData)
#' 
#' # Load in samples
#' fs <- Activation
#' gs <- GatingSet(fs)
#' 
#' # Apply compensation
#' gs <- compensate(gs, fs[[1]]@description$SPILL)
#' 
#' # Transform fluorescent channels
#' trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
#' gs <- transform(gs, trans)
#' 
#' # Gate using gate_draw
#' gating(Activation_gatingTemplate, gs)
#' 
#' # Plot
#' cyto_plot(gs[[4]],
#'   parent = "root",
#'   channels = c("FSC-A", "SSC-A")
#' )
#' 
#' # Cells gate
#' cyto_plot_gate(getGate(gs, "Cells")[[1]],
#'   channels = c("FSC-A", "SSC-A"),
#'   gate_line_col = "purple"
#' )
#' @export
setMethod(cyto_plot_gate,
  signature = "polygonGate",
  definition = function(x,
                          channels,
                          gate_line_type = 1,
                          gate_line_width = 2.5,
                          gate_line_col = "red",
                          gate_point = FALSE,
                          gate_point_shape = 16,
                          gate_point_size = 1) {

    # Assign x to gt
    gt <- x

    # Check Channels
    if (missing(channels)) {
      channels <- as.vector(parameters(gt))
    }

    if (!all(as.vector(parameters(gt)) %in% channels)) {
      stop(paste(
        "Channels argument should contain",
        paste(parameters(gt), collapse = " & "),
        "to plot supplied gate(s)."
      ))
    }

    # Replace Inf values with plot limits
    if (!all(is.finite(gt@boundaries))) {
      cnt <- 0
      lapply(seq_along(channels), function(x) {
        cnt <<- cnt + 1

        if (any(!is.finite(gt@boundaries[, channels[x]]) &
          any(gt@boundaries[, channels[x]] < 0))) {
          if (cnt == 1) {
            ind <- which(gt@boundaries[, channels[x]] < 0)
            gt@boundaries[, channels[x]][ind] <<- par("usr")[1]
          } else if (cnt == 2) {
            ind <- which(gt@boundaries[, channels[x]] < 0)
            gt@boundaries[, channels[x]][ind] <<- par("usr")[3]
          }
        }

        if (any(!is.finite(gt@boundaries[, channels[x]]) &
          any(!gt@boundaries[, channels[x]] < 0))) {
          if (cnt == 1) {
            ind <- which(!is.finite(gt@boundaries[, channels[x]]) &
              !gt@boundaries[, channels[x]] < 0)
            gt@boundaries[, channels[x]][ind] <<- par("usr")[2]
          } else if (cnt == 2) {
            ind <- which(!is.finite(gt@boundaries[, channels[x]]) &
              !gt@boundaries[, channels[x]] < 0)
            gt@boundaries[, channels[x]][ind] <<- par("usr")[4]
          }
        }
      })
    }

    # Plot Gate
    if (gate_point == TRUE) {
      points(
        x = c(gt@boundaries[, channels[1]]),
        y = c(gt@boundaries[, channels[2]]),
        pch = gate_point_shape,
        col = gate_line_col,
        cex = gate_point_size
      )
    }

    polygon(gt@boundaries[, channels[1]],
      gt@boundaries[, channels[2]],
      border = gate_line_col,
      lwd = gate_line_width,
      lty = gate_line_type
    )

    invisible(gt)
  }
)

#' Plot ellipsoidGate Objects onto an Existing Plot
#'
#' @param x an object of class
#'   \code{\link[flowCore:ellipsoidGate-class]{ellipsoidGate}}.
#' @param channels fluorescent channels to used to construct the plot.
#' @param gate_line_type integer [0,6] which controls the line type, set to
#'   \code{1} to draw solid lines by default.
#' @param gate_line_width numeric to adjust line thickness of gates, set to
#'   \code{2.5} by default.
#' @param gate_line_col indicates the colour of the gate to be constructed, set
#'   to \code{"red"} by default.
#' @param gate_point logical indicating whether points should be included when
#'   plotting the gates, set to \code{FALSE} by default.
#' @param gate_point_shape integer [0,25] passed to pch to control the shape of
#'   the points, set to \code{16} to draw filled circles by default. For other
#'   shapes refer to \code{\link[graphics:points]{?pch}}.
#' @param gate_point_size numeric character expansion to control the size of the
#'   points in the drawn gate, set to \code{1} by default.
#'
#' @return gate object with modified co-ordinates for plotting.
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @importFrom flowCore parameters
#' @importFrom methods as
#' @importFrom graphics polygon
#'
#' @seealso \code{\link{cyto_plot_gate,rectangleGate-method}}
#' @seealso \code{\link{cyto_plot_gate,polygonGate-method}}
#' @seealso \code{\link{cyto_plot_gate,list-method}}
#' @seealso \code{\link{cyto_plot_gate,filters-method}}
#'
#' @examples
#' library(CytoRSuiteData)
#' 
#' # Load in samples
#' fs <- Activation
#' gs <- GatingSet(fs)
#' 
#' # Apply compensation
#' gs <- compensate(gs, fs[[1]]@description$SPILL)
#' 
#' # Transform fluorescent channels
#' trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
#' gs <- transform(gs, trans)
#' 
#' # Gate using gate_draw
#' gating(Activation_gatingTemplate, gs)
#' 
#' # Plot
#' cyto_plot(gs[[4]],
#'   parent = "Live Cells",
#'   channels = c("APC-Cy7-A", "PE-A"),
#'   axes_trans = trans
#' )
#' 
#' # T Cells gate
#' cyto_plot_gate(getGate(gs, "T Cells")[[1]],
#'   channels = c("APC-Cy7-A", "PE-A"),
#'   gate_line_col = "purple"
#' )
#' @export
setMethod(cyto_plot_gate,
  signature = "ellipsoidGate",
  definition = function(x,
                          channels,
                          gate_line_type = 1,
                          gate_line_width = 2.5,
                          gate_line_col = "red",
                          gate_point = FALSE,
                          gate_point_shape = 16,
                          gate_point_size = 1) {

    # Assign x to gt
    gt <- x

    # Check Channels
    if (missing(channels)) {
      channels <- as.vector(parameters(gt))
    }

    if (!all(as.vector(parameters(gt)) %in% channels)) {
      stop(paste(
        "Channels argument should contain",
        paste(parameters(gt), collapse = " & "),
        "to plot supplied gate(s)."
      ))
    }

    # Coerce to polygonGate
    gt <- as(gt, "polygonGate")

    # Plot gate
    polygon(gt@boundaries[, channels[1]],
      gt@boundaries[, channels[2]],
      border = gate_line_col,
      lwd = gate_line_width,
      lty = gate_line_type
    )

    invisible(gt)
  }
)

#' Plot List of Gate Objects onto an Existing Plot
#'
#' @param x an object of class \code{list} containing objects of class
#'   \code{rectangleGate}, \code{polygonGate} or \code{ellipsoidGate}.
#' @param channels fluorescent channels to used to construct the plot.
#' @param gate_line_type integer [0,6] which controls the line type, set to
#'   \code{1} to draw solid lines by default.
#' @param gate_line_width numeric to adjust line thickness of gates, set to
#'   \code{2.5} by default.
#' @param gate_line_col indicates the colour of the gate to be constructed, set
#'   to \code{"red"} by default.
#' @param gate_point logical indicating whether points should be included when
#'   plotting the gates, set to \code{FALSE} by default.
#' @param gate_point_shape integer [0,25] passed to pch to control the shape of
#'   the points, set to \code{16} to draw filled circles by default. For other
#'   shapes refer to \code{\link[graphics:points]{?pch}}.
#' @param gate_point_size numeric character expansion to control the size of the
#'   points in the drawn gate, set to \code{1} by default.
#'
#' @return gate object with modified co-ordinates for plotting.
#'
#' @importFrom flowCore parameters
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @seealso \code{\link{cyto_plot_gate,rectangleGate-method}}
#' @seealso \code{\link{cyto_plot_gate,polygonGate-method}}
#' @seealso \code{\link{cyto_plot_gate,ellipsoidGate-method}}
#' @seealso \code{\link{cyto_plot_gate,filters-method}}
#'
#' @examples
#' library(CytoRSuiteData)
#' 
#' # Load in samples
#' fs <- Activation
#' gs <- GatingSet(fs)
#' 
#' # Apply compensation
#' gs <- compensate(gs, fs[[1]]@description$SPILL)
#' 
#' # Transform fluorescent channels
#' trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
#' gs <- transform(gs, trans)
#' 
#' # Gate using gate_draw
#' gating(Activation_gatingTemplate, gs)
#' 
#' # Plot
#' cyto_plot(gs[[4]],
#'   parent = "Live Cells",
#'   channels = c("APC-Cy7-A", "PE-A"),
#'   axes_trans = trans
#' )
#' 
#' # T Cells & Dendritic Cells gate
#' cyto_plot_gate(list(
#'   getGate(gs, "T Cells")[[1]],
#'   getGate(gs, "Dendritic Cells")[[1]]
#' ),
#' channels = c("APC-Cy7-A", "PE-A"),
#' gate_line_col = c("purple", "magenta")
#' )
#' @export
setMethod(cyto_plot_gate,
  signature = "list",
  definition = function(x,
                          channels,
                          gate_line_type = 1,
                          gate_line_width = 2.5,
                          gate_line_col = "red",
                          gate_point = FALSE,
                          gate_point_shape = 16,
                          gate_point_size = 1) {

    # Assign x to gts
    gts <- x

    # Check Channels
    if (missing(channels)) {
      channels <- unique(unlist(lapply(gts, "parameters")))
    }

    # Gate colours
    if (length(gate_line_col) != length(gts)) {
      if (length(gate_line_col) == 1) {
        gate_line_col <- rep(gate_line_col, length(gts))
      } else if (length(gate_line_col) > length(gts)) {
        gate_line_col <- gate_line_col[seq_len(length(gts))]
      }
    }

    # Gate Line Type
    if (length(gate_line_type) != length(gts)) {
      if (length(gate_line_type) == 1) {
        gate_line_type <- rep(gate_line_type, length(gts))
      } else if (length(gate_line_type) > length(gts)) {
        gate_line_type <- gate_line_type[seq_len(length(gts))]
      }
    }

    # Gate Line Width
    if (length(gate_line_width) != length(gts)) {
      if (length(gate_line_width) == 1) {
        gate_line_width <- rep(gate_line_width, length(gts))
      } else if (length(gate_line_width) > length(gts)) {
        gate_line_width <- gate_line_width[seq_len(length(gts))]
      }
    }

    # Gate Point Character
    if (length(gate_point_shape) != length(gts)) {
      if (length(gate_point_shape) == 1) {
        gate_point_shape <- rep(gate_point_shape, length(gts))
      } else if (length(gate_point_shape) > length(gts)) {
        gate_point_shape <- gate_point_shape[seq_len(length(gts))]
      }
    }

    # Gate Point Expansion
    if (length(gate_point_size) != length(gts)) {
      if (length(gate_point_size) == 1) {
        gate_point_size <- rep(gate_point_size, length(gts))
      } else if (length(gate_point_size) > length(gts)) {
        gate_point_size <- gate_point_size[seq_len(length(gts))]
      }
    }

    # Plot Gates
    gts <- mapply(
      function(gt,
                     gate_line_col,
                     gate_line_type,
                     gate_line_width,
                     gate_point_shape,
                     gate_point_size) {
        cyto_plot_gate(gt,
          channels = channels,
          gate_line_col = gate_line_col,
          gate_line_width = gate_line_width,
          gate_line_type = gate_line_type,
          gate_point = gate_point,
          gate_point_shape = gate_point_shape,
          gate_point_size = gate_point_size
        )
      }, gts,
      gate_line_col,
      gate_line_type,
      gate_line_width,
      gate_point_shape,
      gate_point_size
    )

    invisible(gts)
  }
)

#' Plot filters List of Gate Objects onto an Existing Plot
#'
#' @param x an object of class \code{\link[flowCore:filters-class]{filters}}
#'   containing objects of class \code{rectangleGate}, \code{polygonGate} or
#'   \code{ellipsoidGate}.
#' @param channels fluorescent channels to used to construct the plot.
#' @param gate_line_type integer [0,6] which controls the line type, set to
#'   \code{1} to draw solid lines by default.
#' @param gate_line_width numeric to adjust line thickness of gates, set to
#'   \code{2.5} by default.
#' @param gate_line_col indicates the colour of the gate to be constructed, set
#'   to \code{"red"} by default.
#' @param gate_point logical indicating whether points should be included when
#'   plotting the gates, set to \code{FALSE} by default.
#' @param gate_point_shape integer [0,25] passed to pch to control the shape of
#'   the points, set to \code{16} to draw filled circles by default. For other
#'   shapes refer to \code{\link[graphics:points]{?pch}}.
#' @param gate_point_size numeric character expansion to control the size of the
#'   points in the drawn gate, set to \code{1} by default.
#'
#'
#' @return gate object with modified co-ordinates for plotting.
#'
#' @importFrom flowCore parameters
#'
#' @author Dillon Hammill, \email{Dillon.Hammill@anu.edu.au}
#'
#' @seealso \code{\link{cyto_plot_gate,rectangleGate-method}}
#' @seealso \code{\link{cyto_plot_gate,polygonGate-method}}
#' @seealso \code{\link{cyto_plot_gate,ellipsoidGate-method}}
#' @seealso \code{\link{cyto_plot_gate,list-method}}
#'
#' @examples
#' library(CytoRSuiteData)
#' 
#' # Load in samples
#' fs <- Activation
#' gs <- GatingSet(fs)
#' 
#' # Apply compensation
#' gs <- compensate(gs, fs[[1]]@description$SPILL)
#' 
#' # Transform fluorescent channels
#' trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
#' gs <- transform(gs, trans)
#' 
#' # Gate using gate_draw
#' gating(Activation_gatingTemplate, gs)
#' 
#' # Plot
#' cyto_plot(gs[[4]],
#'   parent = "Live Cells",
#'   channels = c("APC-Cy7-A", "PE-A"),
#'   axes_trans = trans
#' )
#' 
#' # T Cells & Dendritic Cells gate
#' cyto_plot_gate(filters(list(
#'   getGate(gs, "T Cells")[[1]],
#'   getGate(gs, "Dendritic Cells")[[1]]
#' )),
#' channels = c("APC-Cy7-A", "PE-A"),
#' gate_line_col = c("green4", "orange")
#' )
#' @export
setMethod(cyto_plot_gate,
  signature = "filters",
  definition = function(x,
                          channels,
                          gate_line_type = 1,
                          gate_line_width = 2.5,
                          gate_line_col = "red",
                          gate_point = FALSE,
                          gate_point_shape = 16,
                          gate_point_size = 1) {

    # Assign x to gts
    gts <- x

    # Check Channels
    if (missing(channels)) {
      channels <- unique(unlist(lapply(gts, "parameters")))
    }

    # Gate colours
    if (length(gate_line_col) != length(gts)) {
      if (length(gate_line_col) == 1) {
        gate_line_col <- rep(gate_line_col, length(gts))
      } else if (length(gate_line_col) > length(gts)) {
        gate_line_col <- gate_line_col[seq_len(length(gts))]
      }
    }

    # Gate Line Type
    if (length(gate_line_type) != length(gts)) {
      if (length(gate_line_type) == 1) {
        gate_line_type <- rep(gate_line_type, length(gts))
      } else if (length(gate_line_type) > length(gts)) {
        gate_line_type <- gate_line_type[seq_len(length(gts))]
      }
    }

    # Gate Line Width
    if (length(gate_line_width) != length(gts)) {
      if (length(gate_line_width) == 1) {
        gate_line_width <- rep(gate_line_width, length(gts))
      } else if (length(gate_line_width) > length(gts)) {
        gate_line_width <- gate_line_width[seq_len(length(gts))]
      }
    }

    # Gate Point Character
    if (length(gate_point_shape) != length(gts)) {
      if (length(gate_point_shape) == 1) {
        gate_point_shape <- rep(gate_point_shape, length(gts))
      } else if (length(gate_point_shape) > length(gts)) {
        gate_point_shape <- gate_point_shape[seq_len(length(gts))]
      }
    }

    # Gate Point Expansion
    if (length(gate_point_size) != length(gts)) {
      if (length(gate_point_size) == 1) {
        gate_point_size <- rep(gate_point_size, length(gts))
      } else if (length(gate_point_size) > length(gts)) {
        gate_point_size <- gate_point_size[seq_len(length(gts))]
      }
    }

    # Plot Gates
    gts <- mapply(
      function(gt,
                     gate_line_col,
                     gate_line_type,
                     gate_line_width,
                     gate_point_shape,
                     gate_point_size) {
        cyto_plot_gate(gt,
          channels = channels,
          gate_line_col = gate_line_col,
          gate_line_width = gate_line_width,
          gate_line_type = gate_line_type,
          gate_point = gate_point,
          gate_point_shape = gate_point_shape,
          gate_point_size = gate_point_size
        )
      }, gts,
      gate_line_col,
      gate_line_type,
      gate_line_width,
      gate_point_shape,
      gate_point_size
    )

    invisible(gts)
  }
)