From d0311a9a8a9fe3a9cb3d83cae4b2e5a2fee042d5 Mon Sep 17 00:00:00 2001
From: edward-burn <9583964+edward-burn@users.noreply.github.com>
Date: Thu, 14 Nov 2024 15:02:07 +0000
Subject: [PATCH] some tweaks

---
 inst/shiny/scripts/preprocess.R | 57 ++++++++++++++++-----------------
 inst/shiny/server.R             |  1 -
 inst/shiny/ui.R                 | 44 ++++++++++++++++++-------
 3 files changed, 61 insertions(+), 41 deletions(-)

diff --git a/inst/shiny/scripts/preprocess.R b/inst/shiny/scripts/preprocess.R
index 34e79ba..89e349d 100644
--- a/inst/shiny/scripts/preprocess.R
+++ b/inst/shiny/scripts/preprocess.R
@@ -31,9 +31,9 @@ data <- omopgenerics::importSummarisedResult(file.path(getwd(),"data", "raw")) |
 #
 choices <- getChoices(data, flatten = TRUE)
 #
-# # remove matched cohorts from choices
-# choices$summarise_characteristics_grouping_cohort_name <- choices$summarise_characteristics_grouping_cohort_name[
-#   !stringr::str_detect(choices$summarise_characteristics_grouping_cohort_name, "matched")]
+# remove matched cohorts from choices
+choices$summarise_characteristics_grouping_cohort_name <- choices$summarise_characteristics_grouping_cohort_name[
+  !stringr::str_detect(choices$summarise_characteristics_grouping_cohort_name, "matched")]
 #
 settingsUsed <- unique(settings(data) |> pull("result_type"))
 dataFiltered <- list()
@@ -50,36 +50,35 @@ for(i in seq_along(settingsUsed)){
 #
 selected <- choices
 #
-# selected$summarise_characteristics_grouping_cohort_name <- selected$summarise_characteristics_grouping_cohort_name[1]
-# selected$summarise_large_scale_characteristics_grouping_cohort_name <- selected$summarise_large_scale_characteristics_grouping_cohort_name[1]
+selected$summarise_characteristics_grouping_cohort_name <- selected$summarise_characteristics_grouping_cohort_name[1]
+selected$summarise_large_scale_characteristics_grouping_cohort_name <- selected$summarise_large_scale_characteristics_grouping_cohort_name[1]
 #
 # choices$cohort_code_use_grouping_cohort_name <- codeUseCohorts
 # selected$cohort_code_use_grouping_cohort_name <- codeUseCohorts[1]
 #
-# choices$compare_large_scale_characteristics_grouping_cdm_name <- choices$summarise_large_scale_characteristics_grouping_cdm_name
-# choices$compare_large_scale_characteristics_grouping_cohort_1 <- choices$summarise_large_scale_characteristics_grouping_cohort_name
-# choices$compare_large_scale_characteristics_grouping_cohort_2 <- choices$summarise_large_scale_characteristics_grouping_cohort_name
-# selected$compare_large_scale_characteristics_grouping_cdm_name <- choices$compare_large_scale_characteristics_grouping_cdm_name
-# selected$compare_large_scale_characteristics_grouping_cohort_1 <- choices$compare_large_scale_characteristics_grouping_cohort_1[1]
-# selected$compare_large_scale_characteristics_grouping_cohort_2 <- choices$compare_large_scale_characteristics_grouping_cohort_1[2]
-#
-# choices$summarise_large_scale_characteristics_grouping_domain <- settings(dataFiltered$summarise_large_scale_characteristics) |>
-#   pull("table_name")
-# selected$summarise_large_scale_characteristics_grouping_domain <- choices$summarise_large_scale_characteristics_grouping_domain
-#
-# choices$summarise_large_scale_characteristics_grouping_time_window <- unique(dataFiltered$summarise_large_scale_characteristics |>
-#   pull("variable_level"))
-# selected$summarise_large_scale_characteristics_grouping_time_window <-choices$summarise_large_scale_characteristics_grouping_time_window
-#
-# orphanCodelist <- unique(dataFiltered$orphan_code_use |>
-#                            visOmopResults::splitAll() |> pull("codelist_name"))
-# orphanCdm <- unique(dataFiltered$orphan_code_use |>
-#                             visOmopResults::addSettings() |> pull("cdm_name"))
-#
-# choices$orphan_grouping_cdm_name <- orphanCdm
-# choices$orphan_grouping_codelist_name <- orphanCodelist
-# selected$orphan_grouping_cdm_name <- orphanCdm
-# selected$orphan_grouping_cohort_name <- orphanCodelist[1]
+choices$compare_large_scale_characteristics_grouping_cdm_name <- choices$summarise_large_scale_characteristics_grouping_cdm_name
+choices$compare_large_scale_characteristics_grouping_cohort_1 <- choices$summarise_large_scale_characteristics_grouping_cohort_name
+choices$compare_large_scale_characteristics_grouping_cohort_2 <- choices$summarise_large_scale_characteristics_grouping_cohort_name
+selected$compare_large_scale_characteristics_grouping_cdm_name <- choices$compare_large_scale_characteristics_grouping_cdm_name
+selected$compare_large_scale_characteristics_grouping_cohort_1 <- choices$compare_large_scale_characteristics_grouping_cohort_1[1]
+selected$compare_large_scale_characteristics_grouping_cohort_2 <- choices$compare_large_scale_characteristics_grouping_cohort_1[2]
+
+choices$summarise_large_scale_characteristics_grouping_domain <- settings(dataFiltered$summarise_large_scale_characteristics) |>
+  pull("table_name")
+selected$summarise_large_scale_characteristics_grouping_domain <- choices$summarise_large_scale_characteristics_grouping_domain
+
+choices$summarise_large_scale_characteristics_grouping_time_window <- unique(dataFiltered$summarise_large_scale_characteristics |>
+  pull("variable_level"))
+selected$summarise_large_scale_characteristics_grouping_time_window <-choices$summarise_large_scale_characteristics_grouping_time_window
+
+orphanCodelist <- unique(dataFiltered$orphan_code_use |>
+                           visOmopResults::splitAll() |> pull("codelist_name"))
+orphanCdm <- unique(dataFiltered$orphan_code_use |>
+                            visOmopResults::addSettings() |> pull("cdm_name"))
+choices$orphan_grouping_cdm_name <- orphanCdm
+choices$orphan_grouping_codelist_name <- orphanCodelist
+selected$orphan_grouping_cdm_name <- orphanCdm
+selected$orphan_grouping_cohort_name <- orphanCodelist[1]
 #
 # unmappedCodelist <- unique(dataFiltered$unmapped_codes |>
 #                            visOmopResults::splitAll() |> pull("codelist_name"))
diff --git a/inst/shiny/server.R b/inst/shiny/server.R
index b405d0d..e0adb5c 100644
--- a/inst/shiny/server.R
+++ b/inst/shiny/server.R
@@ -884,7 +884,6 @@ server <- function(input, output, session) {
     result <- dataFiltered$orphan_code_use |>
       dplyr::filter(cdm_name %in% input$orphan_grouping_cdm_name,
                     group_level %in% input$orphan_grouping_codelist_name)
-
   tbl <- CodelistGenerator::tableOrphanCodes(
       result,
       header = input$orphan_gt_99_header,
diff --git a/inst/shiny/ui.R b/inst/shiny/ui.R
index fb75edd..158babf 100644
--- a/inst/shiny/ui.R
+++ b/inst/shiny/ui.R
@@ -2,9 +2,8 @@
 # Be careful editing this file
 
 ui <- bslib::page_navbar(
-  theme = bs_theme(bootswatch = "zephyr"),
-
-  #minty pulse
+  theme = bs_theme(bootswatch = "pulse"),
+  #  zephyr
 
   title = "PhenotypeR",
   bslib::nav_panel(
@@ -13,10 +12,11 @@ ui <- bslib::page_navbar(
     shiny::includeMarkdown(path = "background.md")
 
   ),
-
+  # Database diagnostics -----
   bslib::nav_menu(
     title = "Database diagnostics",
     icon = shiny::icon("list"),
+    ## snapshot -----
     bslib::nav_panel(
       title = "Snapshot",
       icon = shiny::icon("clipboard-list"),
@@ -39,6 +39,7 @@ ui <- bslib::page_navbar(
                 gt::gt_output("summarise_omop_snapshot_gt_17") |> withSpinner()
             )
     ),
+    ## observation periods -----
     bslib::nav_panel(
       title = "Observation periods",
       icon = shiny::icon("eye"),
@@ -65,10 +66,17 @@ ui <- bslib::page_navbar(
           )
     )
   ),
-
+  # Codelist diagnostics -----
   bslib::nav_menu(
     title = "Codelist diagnostics",
     icon = shiny::icon("list"),
+    ## achilles code use -----
+    bslib::nav_panel(
+      title = "Achilles Code Use",
+      icon = shiny::icon("database")
+    ),
+
+    ## unmapped concepts -----
     bslib::nav_panel(
       title = "Unmapped concepts",
       icon = shiny::icon("database"),
@@ -146,6 +154,7 @@ ui <- bslib::page_navbar(
       )
     ),
 
+    ## Orphan codes -----
     bslib::nav_panel(
       title = "Orphan codes",
       icon = shiny::icon("circle-half-stroke"),
@@ -222,10 +231,13 @@ ui <- bslib::page_navbar(
 
   ),
 
+  # Cohort diagnostics -----
+
   bslib::nav_menu(
     title = "Cohort diagnostics",
     icon = shiny::icon("list"),
 
+    ## Cohort code use -----
 
     bslib::nav_panel(
       title = "Cohort code use",
@@ -319,7 +331,7 @@ ui <- bslib::page_navbar(
         )
       )
     ),
-
+    ## Cohort characteristics -----
   bslib::nav_panel(
       title = "Cohort characteristics",
       icon = shiny::icon("users-gear"),
@@ -375,9 +387,6 @@ ui <- bslib::page_navbar(
               )
             )
             )
-
-
-
           )
         ),
             bslib::card(
@@ -400,6 +409,8 @@ ui <- bslib::page_navbar(
             )
       )
     ),
+  ## Large scale characteristics -----
+
     bslib::nav_panel(
       title = "Large scale characteristics",
       icon = shiny::icon("arrow-up-right-dots"),
@@ -531,6 +542,7 @@ ui <- bslib::page_navbar(
         )
       )
     ),
+  ## Compare large scale characteristics -----
     bslib::nav_panel(
       title = "Compare large scale characteristics",
       icon = shiny::icon("arrow-up-right-dots"),
@@ -570,8 +582,8 @@ ui <- bslib::page_navbar(
           full_screen = TRUE,
           plotly::plotlyOutput("plotly_compare_lsc") |> withSpinner()
           )
-
       )),
+  ## Cohort overlap -----
     bslib::nav_panel(
       title = "Cohort overlap",
       icon = shiny::icon("circle-half-stroke"),
@@ -742,9 +754,12 @@ ui <- bslib::page_navbar(
       )
     )
   ),
+
+  # Population diagnostics -----
   bslib::nav_menu(
     title = "Population diagnostics",
     icon = shiny::icon("list"),
+    ## Incidence -----
     bslib::nav_panel(
       title = "Incidence",
       icon = shiny::icon("chart-line"),
@@ -918,7 +933,7 @@ ui <- bslib::page_navbar(
           )
         )
       )
-    )
+    ),
     # ,
     # bslib::nav_panel(
     #   title = "Attrition",
@@ -1136,6 +1151,12 @@ ui <- bslib::page_navbar(
     #     )
     #   )
     # )
+    
+    ## Prevalence -----
+    bslib::nav_panel(
+      title = "Prevalence",
+      icon = shiny::icon("chart-line")
+    )
   ),
   bslib::nav_spacer(),
   bslib::nav_item(
@@ -1148,4 +1169,5 @@ ui <- bslib::page_navbar(
       )
     )
   )
+  # end ------
 )