Merge pull request #27 from william-hutchison/upgrade-gating

Upgrade gating

.Rbuildignore

@@ -1,20 +1,2 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-
-# Read me
 README.Rmd
-README_files*
-README_cache*
-
-^vignettes/introduction_cache$
-^doc$
-^Meta$
-^codecov\.yml$
-^dev$
-^README_cache$
-^README_files$
-README.Rmd
-^.git$
-.coveralls.yml
-.travis.yml
 .github

DESCRIPTION

@@ -1,26 +1,30 @@
 Package: tidygate
 Type: Package
-Title: Add Gate Information to Your Tibble
-Version: 0.5.3
+Title: Interactively gate points
+Version: 1.0.9
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",
            role = c("aut", "cre"),
            email = "[email protected]"),
       person(given = "Wajid",
              family = "Jawaid",
-             role = "ctb"))
+             role = "ctb"),
+      person(given = "William",
+             family = "Hutchison",
+             role = "aut")
+             )
 Maintainer: Stefano Mangiola <[email protected]>
-Description: It interactively or programmatically label points within custom gates on two dimensions <https://github.com/stemangiola/tidygate>. 
-    The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid (who is also author of this package). The code of 'gatepoints' was nto integrated in 'tidygate'. 
-    The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots; 
-    (ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
+Description: 
+  tidygate allows you to interactively gate points on a scatter plot. Interactively drawn gates are 
+  recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is 
+  based on the package gatepoints by Wajid Jawaid (who is also an author of this package). 
 License: GPL-3
-Depends:
-    R (>= 3.6.0)
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
+Depends:
+    R (>= 3.6.0)
 Imports: 
     utils,
     graphics,
@@ -43,7 +47,8 @@ RdMacros: lifecycle
 Suggests: 
     testthat,
     markdown,
-    knitr
+    knitr,
+    readr
 VignetteBuilder: 
     knitr
 Biarch: true

NAMESPACE

@@ -1,28 +1,33 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(gate,spec_tbl_df)
-S3method(gate,tbl_df)
 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_custom)
 export(gate_int)
-export(gate_simple)
+export(gate_old)
 export(server)
 export(ui)
 import(dplyr)
 import(tibble)
 import(tidyr)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
-importFrom(dplyr,rename)
-importFrom(dplyr,select)
+importFrom(dplyr,pull)
+importFrom(dplyr,summarise)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggplot_build)
+importFrom(ggplot2,guides)
+importFrom(ggplot2,scale_alpha_manual)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_shape_manual)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,axis)
@@ -42,13 +47,14 @@ importFrom(plotly,plotlyOutput)
 importFrom(plotly,renderPlotly)
 importFrom(purrr,imap)
 importFrom(purrr,map)
-importFrom(purrr,map_lgl)
+importFrom(purrr,map_chr)
 importFrom(purrr,pluck)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
 importFrom(rlang,":=")
 importFrom(rlang,enquo)
 importFrom(rlang,env)
+importFrom(rlang,eval_tidy)
 importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_is_symbol)
 importFrom(rlang,quo_is_symbolic)
@@ -57,13 +63,20 @@ importFrom(rlang,quo_squash)
 importFrom(scales,alpha)
 importFrom(scales,rescale)
 importFrom(shiny,actionButton)
+importFrom(shiny,br)
+importFrom(shiny,column)
 importFrom(shiny,fluidPage)
-importFrom(shiny,observe)
+importFrom(shiny,fluidRow)
+importFrom(shiny,h2)
+importFrom(shiny,h5)
+importFrom(shiny,observeEvent)
+importFrom(shiny,renderPrint)
 importFrom(shiny,runApp)
 importFrom(shiny,shinyApp)
 importFrom(shiny,stopApp)
+importFrom(shiny,verbatimTextOutput)
 importFrom(stringr,str_pad)
-importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
+importFrom(utils,globalVariables)
 importFrom(utils,head)
 importFrom(viridis,viridis)

R/data.R

@@ -11,3 +11,8 @@
 #'
 #'
 "gate_list"
+
+#' Demo gate data
+#' 
+#' @keywords data
+"demo_gate_data"

R/fhs.R

@@ -1,11 +1,11 @@
-## Author: Wajid Jawaid
-## Email: [email protected]
-## Date: 14 November 2016
+# Author: Wajid Jawaid
+# Email: [email protected]
+# Date: 14 November 2016
 
-##' Freehand select
-##'
-##' Freehand select function. First generate a 2D plot using R's plot function, 
-##' then select gate region by left clicking. Close polygon by right clicking.
+#' Freehand select
+#'
+#' Freehand select function. First generate a 2D plot using R's plot function, 
+#' then select gate region by left clicking. Close polygon by right clicking.
 ##' The function will return the rownames of the enclosed points by the rownames
 ##' of th co-ordinates given in \code{data}.
 ##' @title Freehand select
@@ -19,6 +19,7 @@
 ##' names parameter is TRUE. If names is FALSE then a logical vector indicating whether points
 ##' are in the polygon is returned.
 ##' @author Wajid Jawaid
+##' @importFrom lifecycle deprecate_warn
 ##' @export
 ##' @examples
 ##' \dontrun{
@@ -29,6 +30,8 @@
 ##' }
 ##' @importFrom graphics locator lines points
 fhs <- function(data, mark = TRUE, names = TRUE, ...) {
+  lifecycle::deprecate_warn("1.0.0", "tidygate::fhs()", with = "tidygate::gate()")
+
   cat("Mark region on plot.\n")
   if (!(is.data.frame(data) || is.matrix(data))) stop("data must be a data frame or matrix")
   if (is.null(rownames(data))) rownames(data) <- 1:nrow(data)

R/functions_OLD.R

@@ -210,7 +210,7 @@ pretty_plot = function(.data,
 #'
 #' @return A tibble with additional columns
 #'
-gate_interactive <-
+gate_interactive_old <-
   function(.data,
            .element,
            .dim1,
@@ -350,7 +350,7 @@ gate_interactive <-
 #'
 #' @return A tibble with additional columns
 #'
-gate_programmatic <- 
+gate_programmatic_old <- 
   function(.data,
            .element,
            .dim1,