Merge pull request #29 from william-hutchison/upgrade-gating

Update gating examples

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tidygate
 Type: Package
 Title: Interactively Gate Points
-Version: 1.0.12
+Version: 1.0.13
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",

NAMESPACE

@@ -4,11 +4,8 @@ S3method(gate_chr,numeric)
 S3method(gate_int,numeric)
 export(fhs)
 export(gate)
-export(gate.spec_tbl_df)
-export(gate.tbl_df)
 export(gate_chr)
 export(gate_int)
-export(gate_old)
 export(server)
 export(ui)
 import(dplyr)

R/fhs.R

@@ -22,11 +22,11 @@
 ##' @importFrom lifecycle deprecate_warn
 ##' @export
 ##' @examples
-##' \dontrun{
-##' x <- cbind(1:10, 1:10)
-##' rownames(x) <- 1:10
-##' plot(x, pch = 16, col = "red")
-##' fhs(x)
+##' if(interactive()) {
+##'   x <- cbind(1:10, 1:10)
+##'   rownames(x) <- 1:10
+##'   plot(x, pch = 16, col = "red")
+##'   fhs(x)
 ##' }
 ##' @importFrom graphics locator lines points
 fhs <- function(data, mark = TRUE, names = TRUE, ...) {

R/gate_app.R

@@ -63,10 +63,11 @@ ui <- shiny::fluidPage(
 #' @export
 server <- function(input, output, session) {
 
-  # Fix CRAN note
+  # Fix CRAN notes
   key <- NULL
   curveNumber <- NULL
   pointNumber <- NULL
+  .gate <- NULL
 
   select_data <- tibble()
   brush_data <- tibble()

R/methods.R

@@ -11,7 +11,7 @@ utils::globalVariables(c(".key", ".rs.invokeShinyPaneViewer"))
 #' @importFrom rlang quo_is_null
 #' @importFrom magrittr "%>%"
 #' @importFrom lifecycle deprecate_warn
-#'
+#' 
 #' @name gate_chr
 #'
 #'
@@ -30,19 +30,15 @@ utils::globalVariables(c(".key", ".rs.invokeShinyPaneViewer"))
 #'
 #' @return An character vector, with "0" for elements outside gates and "1..N" for the elements inside the N gates. 
 #'
-#'
 #' @examples
 #'
-#' \dontrun{
 #' # Standard use - interactive
 #' 
-#'   if(interactive()){
-#'
-#'  tidygate::tidygate_data  %>%
-#'  distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
-#'  mutate(gate = gate_chr( Dim1, Dim2)) 
+#' if(interactive()){
 #'
-#'   }
+#'   tidygate::tidygate_data  %>%
+#'     distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+#'     mutate(gate = gate_chr( Dim1, Dim2)) 
 #'
 #' }
 #'
@@ -227,11 +223,6 @@ gate_int.numeric = 	function(  .dim1,
 #' point size, either a numeric or factor of 6 or less levels.
 #' @return A vector of strings, of the gates each X and Y coordinate pair is within. If gates are
 #' drawn interactively, they are temporarily saved to `tidygate_env$gates`
-#' @examples
-#' \dontrun{
-#' mtcars |>
-#'   mutate(selected = gate_interactive(x = mpg, y = wt, shape = am))
-#'}
 gate_interactive <-
   function(x, y, colour = NULL, shape = NULL, alpha = 1, size = 2) {
 
@@ -467,15 +458,18 @@ gate_programmatic <-
 #' @return A vector of strings, of the gates each X and Y coordinate pair is within. If gates are
 #' drawn interactively, they are temporarily saved to `tidygate_env$gates`.
 #' @examples 
-#' \dontrun{
+#' library(dplyr)
+#' data("demo_gate_data", package = "tidygate")
+#' 
 #' # Gate points interactively
-#' mtcars |>
-#'   mutate(gated = gate(x = mpg, y = wt, shape = am))
+#' if(interactive()) {
+#'   mtcars |>
+#'     mutate(gated = gate(x = mpg, y = wt, shape = am))
+#' }
 #' 
 #' # Gate points programmatically
 #' mtcars |>
-#'   mutate(gated = gate(x = mpg, y = wt, programmatic_gates = tidygate_env$programmatic_gates))
-#'}
+#'   mutate(gated = gate(x = mpg, y = wt, programmatic_gates = demo_gate_data))
 #' @export
 gate <-
   function(x, y, colour = NULL, shape = NULL, alpha = 1, size = 2, programmatic_gates = NULL) {