Clean things up for readability. (#287)

* Clean things up for readability. * Add gt to Imports to elevate from gsm Suggests.
Gilead-BioStats · Oct 16, 2024 · 73f8b0f · 73f8b0f
1 parent af109b8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,6 +23,7 @@ Imports:
     DT,
     glue,
     gsm (>= 2.1.0),
+    gt,
     htmltools,
     htmlwidgets,
     jsonlite,

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,6 +7,7 @@ export(sample_FetchParticipantData)
 import(shiny)
 importFrom(cli,cli_alert)
 importFrom(cli,cli_alert_info)
+importFrom(gt,gt)
 importFrom(kableExtra,kbl)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
diff --git a/R/aaa-shared.R b/R/aaa-shared.R
@@ -23,6 +23,8 @@
 #' @param dfGroups `data.frame` Group-level metadata dictionary.
 #' @param dfMetrics `data.frame` Metric-specific metadata for use in charts and
 #'   reporting.
+#' @param dfParticipantGroups `data.frame` Unique `SubjectID` and `GroupID`
+#'   combos from `dfAnalyticsInput`.
 #' @param dfResults `data.frame` A stacked summary of analysis pipeline output.
 #'   This will be filtered to cases where `GroupLevel == "Site"`.
 #' @param envCall `environment` The environment from which this function was

diff --git a/R/gsm.app-package.R b/R/gsm.app-package.R
@@ -5,6 +5,7 @@
 #' @import shiny
 #' @importFrom cli cli_alert
 #' @importFrom cli cli_alert_info
+#' @importFrom gt gt
 #' @importFrom kableExtra kbl
 #' @importFrom rlang .data
 ## usethis namespace: end

diff --git a/R/gsmApp_Server.R b/R/gsmApp_Server.R
@@ -4,82 +4,57 @@
 #' @returns The main server function for use in a shiny app.
 #' @keywords internal
 gsmApp_Server <- function(
-  dfResults,
+  dfAnalyticsInput,
+  dfBounds,
   dfGroups,
   dfMetrics,
-  dfBounds,
-  dfAnalyticsInput,
+  dfResults,
   fnFetchParticipantData,
   fnServer = NULL
 ) {
   # Force evaluation of everything before factory is constructed to avoid
   # strange effects from lazy evaluation. See
   # https://adv-r.hadley.nz/function-factories.html#forcing-evaluation
-  force(dfResults)
+  force(dfAnalyticsInput)
+  force(dfBounds)
   force(dfGroups)
   force(dfMetrics)
-  force(dfBounds)
-  force(dfAnalyticsInput)
+  force(dfResults)
   force(fnFetchParticipantData)
   force(fnServer)
   function(input, output, session) {
     if (!is.null(fnServer)) {
       fnServer(input, output, session)
     }
 
-    # Inputs ----
-    ## Initialize ----
-    dfAnalyticsInput_Unique <- dfAnalyticsInput %>%
-      dplyr::distinct(.data$SubjectID, .data$GroupID) %>%
-      dplyr::arrange(.data$SubjectID)
-    chrParticipantIDs <- dfAnalyticsInput_Unique$SubjectID
-
-    ## Reset ----
-    observe({
-      updateSelectInput(session, "metric", selected = dfMetrics$MetricID[[1]])
-      updateSelectInput(session, "site", selected = "None")
-      updateSelectizeInput(
-        "participant",
-        choices = c("None", chrParticipantIDs),
-        selected = "None",
-        server = TRUE,
-        session = session
-      )
-      bslib::nav_select("primary_nav_bar", "Study Overview")
-    }) %>%
-      bindEvent(input$reset)
+    # Reset ----
+    dfParticipantGroups <- make_dfParticipantGroups(dfAnalyticsInput)
+    srvr_Reset(dfMetrics, dfParticipantGroups, reactive(input$reset), session)
 
     # Shared Reactives ----
 
+    ## Inputs pass to modules (etc) as reactives.
+    rctv_InputMetric <- reactive(input$metric)
+    rctv_InputSite <- reactive(input$site)
+
     ## The listified dfMetrics are used by both metric sub-mods, so calculate
     ## them once. This can/should move inside a single metric-tab module.
-    rctv_lMetric_base <- reactive({
-      as.list(
-        filter_byMetricID(dfMetrics, input$metric)
-      )
-    }) %>%
-      bindCache(input$metric)
-    rctv_lMetric <- reactive({
-      lMetric <- rctv_lMetric_base()
-      if (input$site != "None") {
-        lMetric$selectedGroupIDs <- input$site
-      }
-      lMetric
-    }) %>%
-      shiny::bindCache(input$metric, input$site)
-
-    rctv_chrParticipantIDs <- reactive({
-      if (input$site == "None") {
-        return(c("None", dfAnalyticsInput_Unique$SubjectID))
-      }
-      c(
-        "None",
-        dfAnalyticsInput_Unique$SubjectID[
-          dfAnalyticsInput_Unique$GroupID == input$site
-        ]
-      )
-    }) %>%
-      bindCache(input$site)
+    rctv_lMetric_base <- srvr_rctv_lMetric_base(
+      dfMetrics,
+      rctv_InputMetric,
+      session
+    )
+    rctv_lMetric <- srvr_rctv_lMetric(
+      dfMetrics,
+      rctv_lMetric_base,
+      rctv_InputMetric,
+      rctv_InputSite,
+      session
+    )
+    rctv_chrParticipantIDs <- srvr_rctv_chrParticipantIDs(
+      dfParticipantGroups,
+      rctv_InputSite
+    )
 
     # Tab Contents ----
 
@@ -90,7 +65,7 @@ gsmApp_Server <- function(
       dfGroups = dfGroups,
       dfMetrics = dfMetrics,
       dfBounds = dfBounds,
-      rctv_strSiteID = reactive(input$site)
+      rctv_strSiteID = rctv_InputSite
     )
     srvr_SyncSelectInput(
       "site",
@@ -104,44 +79,33 @@ gsmApp_Server <- function(
     )
 
     ## Metric Details ----
-    srvr_SyncTab(
-      "primary_nav_bar",
-      "Metric Details",
-      reactive(input$metric),
-      session
+    srvr_SyncTab("primary_nav_bar", "Metric Details", rctv_InputMetric, session)
+    rctv_strMetricDetailsGroup <- mod_MetricDetails_Server(
+      "metric_details",
+      dfResults = dfResults,
+      dfGroups = dfGroups,
+      dfBounds = dfBounds,
+      rctv_lMetric = rctv_lMetric,
+      rctv_strSiteID = rctv_InputSite,
+      rctv_strMetricID = rctv_InputMetric
     )
-    ## Don't render until it loads. We should be able to fix this later once
-    ## nested-modules are implemented cleanly.
-    bindEvent(
-      {
-        rctv_strMetricDetailsGroup <- mod_MetricDetails_Server(
-          "metric_details",
-          dfResults = dfResults,
-          dfGroups = dfGroups,
-          dfBounds = dfBounds,
-          rctv_lMetric = rctv_lMetric,
-          rctv_strSiteID = reactive(input$site),
-          rctv_strMetricID = reactive(input$metric)
-        )
-        rctv_strSiteDetailsParticipant <- mod_SiteDetails_Server(
-          "site_details",
-          dfGroups = dfGroups,
-          dfAnalyticsInput = dfAnalyticsInput,
-          rctv_strSiteID = reactive(input$site),
-          rctv_strMetricID = reactive(input$metric),
-          rctv_lMetric = rctv_lMetric
-        )
-      },
-      input$primary_nav_bar == "Metric Details",
-      ignoreInit = TRUE,
-      once = TRUE
+    rctv_strSiteDetailsParticipant <- mod_SiteDetails_Server(
+      "site_details",
+      dfGroups = dfGroups,
+      dfAnalyticsInput = dfAnalyticsInput,
+      rctv_strSiteID = rctv_InputSite,
+      rctv_strMetricID = rctv_InputMetric,
+      rctv_lMetric = rctv_lMetric
     )
     srvr_SyncSelectInput("site", rctv_strMetricDetailsGroup, session)
 
     # Temporary: Update Site drop-down when one of the non-module widgets
     # changes its value without sending a full Shiny event.
-    srvr_SyncSelectInput("site", reactive(input$site), session)
+    srvr_SyncSelectInput("site", rctv_InputSite, session)
 
+    ### Sync participant dropdown filter ----
+    ###
+    ### Revisit as app becomes fully modularized.
     rctv_LatestParticipant <- reactiveVal("None")
     observe({
       req(input$participant)
@@ -207,7 +171,6 @@ gsmApp_Server <- function(
     srvr_SyncTab(
       "primary_nav_bar",
       "Participant Details",
-      # reactive(input$participant),
       rctv_LatestParticipant,
       session
     )

diff --git a/R/gsmApp_UI.R b/R/gsmApp_UI.R
@@ -6,14 +6,15 @@
 #' @returns A Shiny UI object
 #' @keywords internal
 gsmApp_UI <- function(
-  dfResults,
-  dfMetrics,
+  dfAnalyticsInput,
   dfGroups,
-  intNParticipants,
+  dfMetrics,
+  dfResults,
   strTitle = "GSM Deep Dive",
   tagListSidebar = NULL
 ) {
   # Transform data for use in lower-level functions. ----
+  intNParticipants <- length(unique(dfAnalyticsInput$SubjectID))
   lStudy <- make_lStudy(dfGroups, dfResults)
   chrMetrics <- rlang::set_names(dfMetrics$MetricID, dfMetrics$Metric)
   chrSites <- sort(unique(dfGroups$GroupID[dfGroups$GroupLevel == "Site"]))

diff --git a/R/mod_SiteDetails_Server.R b/R/mod_SiteDetails_Server.R
@@ -56,8 +56,6 @@ mod_SiteDetails_Server <- function(
 
     # This code will be removed in an upcoming update (when these are treated as
     # proper modules).
-    #
-    # nocov start
     observe({
       if (rctv_strSiteID() == "None") {
         ## Show placeholders
@@ -77,7 +75,6 @@ mod_SiteDetails_Server <- function(
         shinyjs::show("card_participants")
       }
     })
-    # nocov end
 
     ### Site Metadata
     output$site_metadata_list <- renderUI({

diff --git a/R/run_gsm_app.R b/R/run_gsm_app.R
@@ -18,42 +18,42 @@
 #' run_sample_gsm_app()
 #' @export
 run_gsm_app <- function(
-  dfResults,
+  dfAnalyticsInput,
+  dfBounds,
   dfGroups,
   dfMetrics,
-  dfBounds,
-  dfAnalyticsInput,
+  dfResults,
   fnFetchParticipantData,
   strTitle = "GSM Deep Dive",
   tagListSidebar = NULL,
   fnServer = NULL
 ) {
   # There's no point launching the app if the data won't work.
-  dfResults <- validate_dfResults(dfResults)
+  dfAnalyticsInput <- validate_dfAnalyticsInput(dfAnalyticsInput)
+  dfBounds <- validate_dfBounds(dfBounds)
   dfGroups <- validate_dfGroups(dfGroups)
   dfMetrics <- validate_dfMetrics(dfMetrics)
-  dfBounds <- validate_dfBounds(dfBounds)
-  dfAnalyticsInput <- validate_dfAnalyticsInput(dfAnalyticsInput)
+  dfResults <- validate_dfResults(dfResults)
 
   # We currently only use site-level data in this app.
-  dfResults <- dfResults[dfResults$GroupLevel == "Site", ]
   dfAnalyticsInput <- dfAnalyticsInput[dfAnalyticsInput$GroupLevel == "Site", ]
+  dfResults <- dfResults[dfResults$GroupLevel == "Site", ]
 
   shinyApp(
     ui = gsmApp_UI(
-      dfResults = dfResults,
-      dfMetrics = dfMetrics,
+      dfAnalyticsInput = dfAnalyticsInput,
       dfGroups = dfGroups,
-      intNParticipants = length(unique(dfAnalyticsInput$SubjectID)),
+      dfMetrics = dfMetrics,
+      dfResults = dfResults,
       strTitle = strTitle,
       tagListSidebar = tagListSidebar
     ),
     server = gsmApp_Server(
-      dfResults = dfResults,
+      dfAnalyticsInput = dfAnalyticsInput,
+      dfBounds = dfBounds,
       dfGroups = dfGroups,
       dfMetrics = dfMetrics,
-      dfBounds = dfBounds,
-      dfAnalyticsInput = dfAnalyticsInput,
+      dfResults = dfResults,
       fnFetchParticipantData = fnFetchParticipantData,
       fnServer = fnServer
     )
@@ -64,12 +64,12 @@ run_gsm_app <- function(
 #' @export
 run_sample_gsm_app <- function() { # nocov start
   run_gsm_app(
-    dfResults = gsm.app::sample_dfResults,
+    dfAnalyticsInput = gsm.app::sample_dfAnalyticsInput,
+    dfBounds = gsm.app::sample_dfBounds,
     dfGroups = gsm.app::sample_dfGroups,
     dfMetrics = gsm.app::sample_dfMetrics,
-    dfBounds = gsm.app::sample_dfBounds,
-    dfAnalyticsInput = gsm.app::sample_dfAnalyticsInput,
-    fnFetchParticipantData = gsm.app::sample_FetchParticipantData,
+    dfResults = gsm.app::sample_dfResults,
+    fnFetchParticipantData = sample_FetchParticipantData,
     strTitle = "Sample Deep Dive App"
   )
 } # nocov end