add 'dirty' variable to plate, let user know when they're using a pla…

…te with new settings that need to re-run; fixes #6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ddpcr
 Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
-Version: 1.1.2
+Version: 1.2.0
 Authors@R: c(
     person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"))
     )

NAMESPACE

@@ -72,6 +72,7 @@ export(get_wells_btwn)
 export(has_signif_negative_cluster)
 export(has_step)
 export(is_dir)
+export(is_dirty)
 export(is_empty_plate)
 export(is_file)
 export(is_range)

NEWS.md

@@ -0,0 +1,7 @@
+# shinyjs 1.2.0
+
+2016-03-22
+
+- Added a 'dirty' bit to a plate, to keep track of whether any changes to the settings have been made that require a re-run of the analysis.  Both the shiny app and the command line inform the user if they are using a dirty plate object
+
+- A few bug fixes in the shiny app (don't show in Advanced Settings section the settings that are already shown in Basic Settings, don't show Advanced Settings parameters of other plate types)

R/plate-attribs.R

@@ -270,6 +270,12 @@ params <- function(plate, category, name) {
 #' @export
 `params<-` <- function(plate, category, name, value) {
   stopifnot(plate %>% inherits("ddpcr_plate"))
+
+  # If a setting is changed after any analysis steps took place, mark the
+  # plate as 'dirty'
+  if (!is_empty_plate(plate) && status(plate) > step(plate, "INITIALIZE")) {
+    plate[['dirty']] <- TRUE
+  }
 
   replace <- 'params'
   if (!missing(category)) {
@@ -552,3 +558,14 @@ y_var <- function(plate) {
   params(plate, 'GENERAL', 'Y_VAR') <- value
   plate
 }
+
+#' Is the plate object dirty (ie has changed since the analysis was run)?
+#' @param plate A ddPCR plate
+#' @return \code{TRUE} if any plate settings have changed that require the plate
+#' analysis to re-run; \code{FALSE} otherwise
+#' @keywords internal
+#' @export
+is_dirty <- function(plate) {
+  stopifnot(plate %>% inherits("ddpcr_plate"))
+  plate[['dirty']]
+}

R/plate-print.R

@@ -64,4 +64,8 @@ print.ddpcr_plate <- function(x, ...) {
          "\n"
     )
   }
+
+  if (is_dirty(x)) {
+    cat0("\nNote: some settings have changed, please re-run the analysis with `analyze(plate, restart = TRUE)` for changes to take effect")
+  }
 }

R/plate-utils.R

@@ -14,6 +14,7 @@ empty_plate <- function() {
     params     = NULL,
     clusters   = NULL,
     steps      = NULL,
+    dirty      = NULL,
     version    = NULL
   )
 }
@@ -44,6 +45,7 @@ init_plate <- function(plate) {
 
   status(plate) <- step(plate, 'INITIALIZE')
   plate[['version']] <- as.character(utils::packageVersion("ddpcr"))
+  plate[['dirty']] <- FALSE
   step_end()
 
   plate

R/plate.R

@@ -247,6 +247,7 @@ analyze <- function(plate, restart = FALSE) {
   if (restart) {
     msg("Restarting analysis")
     status(plate) <- 0
+    plate[['dirty']] <- FALSE
   }
   steps_left <- length(steps(plate)) - status(plate)
   plate %<>% next_step(n = steps_left)

R/sample_data.R

@@ -24,9 +24,8 @@ NULL
 
 #' @rdname sample_data
 #' @export
-sample_data_dir <- function(size = c("small", "large")) {
-  size <- match.arg(size)
-  system.file("sample_data", size, package = "ddpcr")
+sample_data_dir <- function() {
+  system.file("sample_data", "small", package = "ddpcr")
 }
 
 #' @rdname sample_data

R/save_load.R

@@ -34,6 +34,7 @@ save_plate <- function(plate, file) {
     params     = params(plate),
     clusters   = clusters(plate),
     steps      = steps(plate),
+    dirty      = plate[['dirty']],
     version    = plate[['version']]
   )
   saveRDS(object = object, file = file)
@@ -66,11 +67,12 @@ load_plate <- function(file) {
     plate_data(plate)  <- object[['plate_data']]
     plate_meta(plate)  <- object[['plate_meta']]
     name(plate)        <- object[['name']]
-    status(plate)      <- object[['status']]
     params(plate)      <- object[['params']]
     clusters(plate)    <- object[['clusters']]
     steps(plate)       <- object[['steps']]
+    plate[['dirty']]   <- object[['dirty']]
     plate[['version']] <- object[['version']]
+    status(plate)      <- object[['status']]
   },
   error = function(err) {
     err_msg(paste("The given file is not a valid ddPCR file",

README.md

@@ -798,7 +798,7 @@ Now we can analyze the plate
 
     #> Classifying droplets...
 
-    #> DONE (0 seconds)
+    #> DONE (1 seconds)
 
     #> Reclassifying droplets... skipped (not enough wells with significant mutant clusters)
 
@@ -1044,6 +1044,7 @@ by running `ddpcr:::init_plate`.
     #>   
     #>   status(plate) <- step(plate, 'INITIALIZE')
     #>   plate[['version']] <- as.character(utils::packageVersion("ddpcr"))
+    #>   plate[['dirty']] <- FALSE
     #>   step_end()
     #>   
     #>   plate

inst/shiny/server.R

@@ -24,7 +24,11 @@ shinyServer(function(input, output, session) {
   # we have a dataset to work with or if we're waiting for dataset to be chosen
   output$datasetChosen <- reactive({ FALSE })
   outputOptions(output, 'datasetChosen', suspendWhenHidden = FALSE)
-
+
+  observeEvent(dataValues$plate, {
+    shinyjs::toggle(id = "plateDirty", condition = is_dirty(dataValues$plate))
+  })
+
   # save button (download dataset) button is clicked
   output$saveBtn <- downloadHandler(
     filename = function() {
@@ -78,10 +82,10 @@ shinyServer(function(input, output, session) {
   # hide the loading message
   hide("loading-content", TRUE, "fade")  
 
-# TODO remove this , for testing purposes only
+#TODO remove this , for testing purposes only
 # dataValues$plate <- new_plate(dir = sample_data_dir(),
 #                               type = plate_types$fam_positive_pnpp)
 # 
-# output$datasetChosen <- reactive({ TRUE })  
+# output$datasetChosen <- reactive({ TRUE })
 # updateTabsetPanel(session, "mainNav", "settingsTab")
 })

inst/shiny/server/tab-settings.R

@@ -128,15 +128,19 @@ observeEvent(input$wellsUsedPlotBrush, {
 # check all advanced settings and save them
 observeEvent(input$updateAdvancedSettings, {
   withBusyIndicator("resetParamsBtn", {
+
     disable("updateAdvancedSettings")
     advanced_param_regex <- "^advanced_setting_param_(.*)__(.*)$"
     all_params <- 
       grep(advanced_param_regex, names(input), value = TRUE)
     lapply(all_params, function(x) {
+
       if (!is.null(input[[x]]) && !is.na(input[[x]])) {
         major_name <- gsub(advanced_param_regex, "\\1", x)
         minor_name <- gsub(advanced_param_regex, "\\2", x)
-        params(dataValues$plate, major_name, minor_name) <- input[[x]]
+        if (!is.null(params(dataValues$plate, major_name, minor_name))) {
+          params(dataValues$plate, major_name, minor_name) <- input[[x]]
+        }
       }
     })
     enable("updateAdvancedSettings")
@@ -167,12 +171,12 @@ observeEvent(dataValues$plate, {
           lapply(
             plate %>% params %>% .[[major_name]] %>% names,
             function(minor_name) {
-              param_name <- sprintf("%s", major_name, minor_name)
+              param_name <- sprintf("%s::%s", major_name, minor_name)
 
               params_ignore <- c(
                 "GENERAL::X_VAR", "GENERAL::Y_VAR",
                 "GENERAL::POSITIVE_NAME", "GENERAL::NEGATIVE_NAME",
-                "CLASSIFY::X_THRESHOLD", "CLASSIFY::Y_THRESHOLD"
+                "GENERAL::POSITIVE_DIMENSION"
               )
 
               if (param_name %in% params_ignore) {

inst/shiny/ui/header.R

@@ -17,7 +17,13 @@ column(
             "droplets"
 
         ),
-        downloadButton('saveBtn', 'Save data', class = "btn-sm")
+        downloadButton('saveBtn', 'Save data', class = "btn-sm"),
+        div(
+          id = "plateDirty",
+          class = "alert alert-danger",
+          strong("Note:"),
+          "Some settings have changed, please re-run the analysis for changes to take effect"
+        )
       )
   )
 )

inst/shiny/www/style.css

@@ -17,6 +17,10 @@ body {
   color: #FFFFFF;
 }
 
+#plateDirty {
+  margin-top: 12px;
+}
+
 .navbar {
   margin-bottom: 0;
 }