Fixes for ggplot2 version 4 and ggcyto breaking changes

DESCRIPTION

@@ -1,15 +1,17 @@
 Package: flowGate
 Type: Package
 Title: Interactive Cytometry Gating in R
-Version: 0.99.2
+Version: 1.13.1
 Authors@R: c(person("Andrew", 
                     "Wight", 
                     email = "andrew.wight10@gmail.com", 
-                    role = c("aut", "cre")),
+                    role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-3116-8722")),
              person("Harvey",
                     "Cantor",
                     email = "Harvey_Cantor@dfci.harvard.edu",
-                    role = c("aut", "ldr")))
+                    role = c("aut", "ldr"),
+           comment = c(ORCID = "0000-0002-3313-2478")))
 Description: flowGate adds an interactive Shiny app to allow manual 
     GUI-based gating of flow cytometry data in R. Using flowGate, 
     you can draw 1D and 2D span/rectangle gates, quadrant gates, 
@@ -19,6 +21,8 @@ Description: flowGate adds an interactive Shiny app to allow manual
     cytometerists looking to take advantage of R for cytometry 
     analysis, without necessarily having a lot of R experience.
 License: MIT + file LICENSE
+URL: https://www.bioconductor.org/packages/release/bioc/html/flowGate.html
+BugReports: https://github.com/NKInstinct/flowGate/issues
 Encoding: UTF-8
 LazyData: false
 Imports:
@@ -34,14 +38,15 @@ Imports:
 Depends:
     flowWorkspace (>= 4.0.6),
     ggcyto (>= 1.16.0),
-    R (>= 4.2)
-RoxygenNote: 7.2.3
+    R (>= 4.4)
+RoxygenNote: 7.3.3
 Suggests: 
     knitr,
     rmarkdown,
     stringr,
     tidyverse,
-    testthat
+    testthat,
+    vdiffr
 VignetteBuilder: knitr
 biocViews:
     Software,
@@ -50,3 +55,4 @@ biocViews:
     Preprocessing,
     ImmunoOncology,
     DataImport
+

NAMESPACE

@@ -1,24 +1,76 @@
 # Generated by roxygen2: do not edit by hand
 
+export(gs_apply_gate_check)
 export(gs_apply_gating_strategy)
 export(gs_gate_interactive)
+export(gs_gate_interactive_adjust)
 export(gs_gate_transform_interactive)
-import(BiocManager)
-import(flowWorkspace)
-import(ggcyto)
+export(gs_to_openCyto)
+importFrom(BiocManager,install)
+importFrom(dplyr,bind_rows)
+importFrom(flowCore,polygonGate)
+importFrom(flowCore,quadGate)
+importFrom(flowCore,rectangleGate)
+importFrom(flowCore,transform_gate)
+importFrom(flowWorkspace,GatingSet)
+importFrom(flowWorkspace,flowjo_biexp)
+importFrom(flowWorkspace,gh_pop_get_gate)
+importFrom(flowWorkspace,gs_get_pop_paths)
+importFrom(flowWorkspace,gs_pop_add)
+importFrom(flowWorkspace,gs_pop_get_gate)
+importFrom(flowWorkspace,gs_pop_get_parent)
+importFrom(flowWorkspace,gs_pop_remove)
+importFrom(flowWorkspace,recompute)
+importFrom(ggcyto,as.ggplot)
+importFrom(ggcyto,geom_gate)
+importFrom(ggcyto,ggcyto)
+importFrom(ggcyto,scale_x_flowjo_biexp)
+importFrom(ggcyto,scale_y_flowjo_biexp)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_)
 importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_density)
 importFrom(ggplot2,geom_hex)
+importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_gray)
 importFrom(methods,is)
+importFrom(openCyto,register_plugins)
+importFrom(purrr,map)
+importFrom(purrr,pluck)
+importFrom(purrr,pmap)
+importFrom(rlang,"!!")
 importFrom(rlang,.data)
+importFrom(shiny,actionButton)
+importFrom(shiny,brushOpts)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,fluidPage)
+importFrom(shiny,mainPanel)
+importFrom(shiny,numericInput)
+importFrom(shiny,observeEvent)
+importFrom(shiny,plotOutput)
+importFrom(shiny,radioButtons)
 importFrom(shiny,reactive)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderText)
+importFrom(shiny,runApp)
+importFrom(shiny,shinyApp)
+importFrom(shiny,sidebarLayout)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,sliderInput)
+importFrom(shiny,stopApp)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tabsetPanel)
+importFrom(shiny,textOutput)
+importFrom(shiny,titlePanel)
 importFrom(shiny,updateTabsetPanel)
+importFrom(stringr,str_equal)
 importFrom(tibble,tribble)
+importFrom(utils,write.csv)

NEWS.md

@@ -1,2 +1,9 @@
-# Changes in version 0.99.2 (2023-03-15)
- - Package cleanup after initial Bioconductor submission
+# Changes in version 0.99.3 (2023-03-15)
+ - Document cleanup as part of bioconductor review
+
+# Changes in version 1.13.1 (2026-07-02)
+ - Implemented fixes due to the ggplot2 version 4 changes, with 
+ the update ggcyto syntax changes
+ - Where appropiate, switched from import to importFrom tags
+ - Implemented gs_apply_gate_check to allow adjustment existing gates
+ - Additional unit tests to test suite

R/applyGateClose.R

@@ -4,6 +4,9 @@
 #' @param gateType The selected type of gate (from UI).
 #' @param filterId The gate name specified by the user.
 #' @param gg The plot object from vars$plot.
+#' 
+#' @importFrom flowCore polygonGate rectangleGate quadGate
+#' @importFrom flowWorkspace gs_pop_add recompute
 #'
 #' @return The original GatingSet with the newly drawn gate applied.
 #'
@@ -12,21 +15,27 @@
 applyGateClose <- function(
     gs, subset, coords, gateType, filterId, gg, useBiex, bins, xMax, xWidth, 
     xPos, xNeg, yMax, yWidth, yPos, yNeg){
+
+    TheNames <- names(gg$data)
+    LastTwo  <- tail(TheNames, 2)
+    FinalOne  <- tail(TheNames, 1)
+
     if(gateType == "polygonGate"){
-        names(coords) <- c(names(gg[[1]])[[3]], names(gg[[1]])[[4]])
+        names(coords) <- LastTwo
         coords <- as.matrix(coords)
         gate <- flowCore::polygonGate(coords, filterId = filterId)
     } else if(gateType == "spanGate"){
-        names(coords) <- c(names(gg[[1]])[[3]])
+        names(coords) <- FinalOne
         gate <- flowCore::rectangleGate(coords, filterId = filterId)
     } else if(gateType == "quadGate"){
-        names(coords) <- c(names(gg[[1]])[[3]], names(gg[[1]])[[4]])
+        names(coords) <- LastTwo
         gate <- flowCore::quadGate(coords, filterId = filterId)
     } else if(gateType == "rectangleGate"){
-        names(coords) <- c(names(gg[[1]])[[3]], names(gg[[1]])[[4]])
+        names(coords) <- LastTwo
         gate <- flowCore::rectangleGate(coords, filterId = filterId)
     }
-    gs_pop_add(gs, gate, parent = subset)
+
+    gs_pop_add(gs=gs, gate=gate, parent = subset)
     recompute(gs)
 
     if(useBiex){

R/applyGateCloseSwap.R

@@ -0,0 +1,63 @@
+#' Apply gate from gs_gate_interactive
+#'
+#' @param coords The coordinates of the interactively drawn gate.
+#' @param gateType The selected type of gate (from UI).
+#' @param filterId The gate name specified by the user.
+#' @param gg The plot object from vars$plot.
+#' @param AdjustAll Default FALSE, applies the gate correction to the entire gating set. 
+#' 
+#' @importFrom flowCore polygonGate rectangleGate quadGate
+#' @importFrom flowWorkspace gs_pop_add recompute
+#'
+#' @return The original GatingSet with the newly drawn gate applied.
+#'
+#' @noRd
+#'
+applyGateCloseSwap <- function(
+    gs, subset, coords, gateType, filterId, gg, useBiex, bins, xMax, xWidth, 
+    xPos, xNeg, yMax, yWidth, yPos, yNeg, sample, AdjustAll=FALSE){
+
+    TheNames <- names(gg$data)
+    LastTwo  <- tail(TheNames, 2)
+    FinalOne  <- tail(TheNames, 1)
+
+    if(gateType == "polygonGate"){
+        names(coords) <- LastTwo
+        coords <- as.matrix(coords)
+        gate <- flowCore::polygonGate(coords, filterId = filterId)
+    } else if(gateType == "spanGate"){
+        names(coords) <- FinalOne
+        gate <- flowCore::rectangleGate(coords, filterId = filterId)
+    } else if(gateType == "quadGate"){
+        names(coords) <- LastTwo
+        gate <- flowCore::quadGate(coords, filterId = filterId)
+    } else if(gateType == "rectangleGate"){
+        names(coords) <- LastTwo
+        gate <- flowCore::rectangleGate(coords, filterId = filterId)
+    }
+
+    # gs_pop_add(gs, gate, parent = subset)
+    TheList <- list(gate)
+
+    if (AdjustAll==FALSE){
+    names(TheList) <- sampleNames(gs[sample])
+    gs_pop_set_gate(gs[sample], filterId, TheList)
+    recompute(gs[sample])
+    } else {
+    TheList <- rep(TheList, length(sampleNames(gs)))
+    names(TheList) <- sampleNames(gs)
+    gs_pop_set_gate(gs, filterId, TheList)
+    recompute(gs)
+    }
+
+    if(useBiex){
+        varsBiex <- list(X = list(
+            maxValue = xMax, widthBasis = xWidth, pos = xPos, neg = xNeg),
+                         Y = list(
+            maxValue = yMax, widthBasis = yWidth, pos = yPos, neg = yNeg))
+    } else{
+        varsBiex <- "unused"
+    }
+    output <- list("Gate" = gate, "Bins" = bins, "Scaling" = varsBiex)
+    return(output)
+    }

R/flowGate-package.R

@@ -0,0 +1,9 @@
+#' @description
+#' To learn more about how to use flowGate, please start by browsing the vignettes:
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/gateHandlers.R

@@ -31,6 +31,16 @@ coordBrush <- function(brush, gateType, useBiex, transX, transY){
     return(res)
 }
 
+#' Internal for Unknown
+#' 
+#' @param click TODOLIST
+#' @param gateType TODOLIST
+#' @param useBiex TODOLIST
+#' @param transX TODOLIST
+#' @param transY TODOLIST
+#' 
+#' @noRd
+#' 
 coordClick <- function(click, gateType, useBiex, transX, transY){
     if(useBiex){
         click$x <- transX(click$x)
@@ -44,6 +54,20 @@ coordClick <- function(click, gateType, useBiex, transX, transY){
     return(res)
 }
 
+#' Internal for Unknown
+#' 
+#' @param gateType TODOLIST
+#' @param brush TODOLIST
+#' @param click TODOLIST
+#' @param biex TODOLIST
+#' @param tX TODOLIST
+#' @param tY TOODOLIST
+#' @param append TODOLIST
+#' 
+#' @importFrom dplyr bind_rows
+#' 
+#' @noRd
+#' 
 gateHandler <- function(gateType, brush, click, biex, tX, tY, append){
     switch(gateType,
             rectangleGate = ,

R/gs_apply_gate_check.R

@@ -0,0 +1,72 @@
+#' The purpose of this function is to allow the readjustment of a gate on an
+#' individual specimen via the Shiny app, quickly iterating through every
+#' specimen present in the GatingSet. 
+#' 
+#' This allows for fine-tuning of the gate placement for non-representative
+#' specimens, or when automated gating methods fail. 
+#'
+#' @param gs A GatingSet or list of GatingSets.
+#' @param gate A tibble-formatted gating strategy (see examples below)
+#' @param sample Sample index in the GatingSet, default NULL will iterate through
+#' all specimens in the GatingSet.
+#' @param AdjustAll Default FALSE, applies the gate correction to the entire gating set. 
+#' @param ... Other parameters to pass to gs_gate_interactive(). Note that only
+#'   constant parameters should be supplied here---anything that varies should
+#'   be included in the gating_strategy tibble.
+#'
+#' @return the GatingSet or list of GatingSets with the gates in gating_strategy
+#'   applied as specified.
+#'
+#' @importFrom tibble tribble
+#' @importFrom methods is
+#' @importFrom purrr pmap
+#'
+#' @examples
+#'
+#' fs <- flowCore::read.flowSet(
+#'   path = system.file("extdata", package = "flowGate"), pattern = ".FCS$")
+#'
+#' gs <- flowWorkspace::GatingSet(fs)
+#'
+#' # Note - this is a very rudamentary GatingSet for example purposes only. 
+#' # Please see the vignette accompanying this package or the flowWorkspace
+#' # documentation # for a complete look at creating a GatingSet.
+#'
+#' gating_strategy <- tibble::tribble(
+#' ~filterId,      ~dims,                       ~subset,        ~coords,
+#' "Lymphocytes", list("FSC-H", "SSC-H"),       "root",         list(c(0, 3e5), c(0, 3e5)),
+#' "CD45 CD15",   list("CD45 PE", "CD15 FITC"), "Lymphocytes",  list(c(0, 3e5), c(0, 2e5)),
+#' )
+#'
+#'
+#' if(interactive()){
+#' gs_apply_gating_strategy(gs,
+#' gating_strategy = gating_strategy,
+#' bins = 512) # note that extra args for gs_gate_interactive can be supplied.
+#' }
+#' @export
+#' 
+gs_apply_gate_check <- function(gs, gate, sample=NULL, AdjustAll=FALSE, ...){
+    if(methods::is(gs, "GatingSet")){
+
+      if(is.null(sample)){
+        Samples <- seq_along(gs)
+      } else {Samples <- sample}
+
+    purrr::walk(
+      .x = Samples,
+      .f = function(sample) {
+        gs_gate_interactive_adjust(
+          gs       = gs,
+          gate = gate,
+          sample   = sample,
+          AdjustAll = AdjustAll,
+          ...
+        )
+      }
+    )
+
+    } else {
+        stop("'gs' must be a GatingSet")
+    }
+}

R/gs_apply_gating_strategy.R

@@ -27,6 +27,7 @@
 #'
 #' @importFrom tibble tribble
 #' @importFrom methods is
+#' @importFrom purrr pmap
 #'
 #' @examples
 #'
@@ -52,10 +53,11 @@
 #' bins = 512) # note that extra args for gs_gate_interactive can be supplied.
 #' }
 #' @export
+#' 
 gs_apply_gating_strategy <- function(gs, gating_strategy, ...){
     if(methods::is(gs, "GatingSet")){
         purrr::pmap(gating_strategy, 
-                    flowGate::gs_gate_interactive, gs = gs, ...)
+                    gs_gate_interactive, gs = gs, ...)
     } else {
         stop("'gs' must be a GatingSet")
     }