#136 move control of fold change labs in patient profile out of mappi…

…ngs tab and into selectize within module
SafetyGraphics · Jun 6, 2024 · a08ca88 · a08ca88
1 parent 942d1df
commit a08ca88
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Showing 5 changed files with 48 additions and 43 deletions.
diff --git a/R/nepexplorerMod.R b/R/nepexplorerMod.R
@@ -14,7 +14,7 @@ nepexplorer_ui <- function(id) {
   sidebar <- sidebarPanel(
     selectizeInput(
       ns("measures"),
-      "Select Measures",
+      "Select Patient Profile Fold Change Measures",
       multiple = TRUE,
       choices = c("")
     ),
@@ -42,6 +42,14 @@ nepexplorer_ui <- function(id) {
 
 
   main <- mainPanel(
+    # HTML header with style specifications.
+    tags$head(
+      tags$style(
+        # hide measure values from mappings tab that we want controlled within "measure" dropdown
+        HTML("div.field-wrap:has(label[id^='sg-mapping-labs-measure_col-measure_values--nepFC_']) { display: none; }"
+        )
+      )
+    ),
     useShinyjs(),
     # Scatter PLot + Summary Table UI
     creatinineScatterUI(ns("scatter")),
@@ -98,15 +106,21 @@ nepexplorer_server <- function(input, output, session, params) {
   })
 
   # Populate sidebar control with measures and select all by default
-  observe({
+  observeEvent(param(), {
     measure_col <- param()$settings$labs$measure_col
     measures <- unique(param()$data[[measure_col]])
+    measure_values <- param()$settings$labs$measure_values
+
+    # go through metadata file and grab measure values with prefix "nepFC"
+    fold_change_measures <- intersect(measures,
+                                      measure_values[grep("nepFC", names(measure_values))])
+
+    # update selectize to reflect what's specific in metadata
     updateSelectizeInput(session,
                          "measures",
                          choices = measures,
-                         selected = measures
+                         selected = fold_change_measures
     )
-
   })
 
   animate <- reactive(input$animate)
@@ -134,7 +148,7 @@ nepexplorer_server <- function(input, output, session, params) {
   #Patient Profile (demo tables + lab line charts)
   observeEvent(selected_subject(), {
     if (length(selected_subject()) == 1) { # avoid triggering patient profiles if there isn't a subject
-      patientProfileServer("patprofile", df = param()$data,
+      patientProfileServer("patprofile", df = param()$data, selected_measures = input$measures,
                            settings = param()$settings, subj_id = selected_subject())
     }
   }, ignoreInit = TRUE)

diff --git a/R/patient_profile_charts.R b/R/patient_profile_charts.R
@@ -180,7 +180,6 @@ drawULNFoldChange <- function(adlb, settings,
                                        "Calcium", "Chloride", "Phosphorus",
                                        "Potassium", "Sodium")) {
 
-
   adlb_FC <- adlb %>%
     filter(.data[[settings$measure_col]] %in% labs) %>%
     group_by(.data[[settings$measure_col]]) %>%

diff --git a/R/patient_profile_mod.R b/R/patient_profile_mod.R
@@ -30,7 +30,7 @@ patientProfileUI <-  function(id) {
 #' @import dplyr
 #' @importFrom plotly renderPlotly
 #' @importFrom magrittr %>%
-patientProfileServer <-  function(id, df, settings, subj_id) {
+patientProfileServer <-  function(id, df, selected_measures, settings, subj_id) {
   moduleServer(
     id,
     function(input, output, session) {
@@ -95,15 +95,7 @@ patientProfileServer <-  function(id, df, settings, subj_id) {
 
       output$ULN_FC <- renderUI({
 
-        default_labs <-  c(lab_settings$measure_values$BICARB,
-                           lab_settings$measure_values$BUN,
-                           lab_settings$measure_values$CA,
-                           lab_settings$measure_values$CL,
-                           lab_settings$measure_values$PHOS,
-                           lab_settings$measure_values$K,
-                           lab_settings$measure_values$SODIUM)
-
-        available_labs <- intersect(patient_df[[lab_settings$measure_col]] %>%  unique(), default_labs)
+        available_labs <- intersect(patient_df[[lab_settings$measure_col]] %>%  unique(), selected_measures)
 
         if (length(available_labs) > 0) {
           drawULNFoldChange(adlb = patient_df, settings = lab_settings,

diff --git a/data-raw/meta_nepExplorer.csv b/data-raw/meta_nepExplorer.csv
@@ -1,27 +1,27 @@
-text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
-id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
-value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
-measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
-studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
-visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
-visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
-measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure 
-measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic  Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
-unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
-vs_baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
-vs_baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
-measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin
-measure_values--Albumin/Creatinine,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
-measure_values--BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
-measure_values--BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
-measure_values--CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
-measure_values--CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
-measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
-measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
-measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
-measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
-measure_values--PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
-measure_values--K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
-measure_values--SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
-baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
-baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y
+text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
+id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
+value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
+measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
+studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
+visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
+visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
+measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure 
+measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic  Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
+unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
+vs_baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
+vs_baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
+measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin
+measure_values--Albumin/Creatinine,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
+measure_values--nepFC_BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
+measure_values--nepFC_BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
+measure_values--nepFC_CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
+measure_values--nepFC_CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
+measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
+measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
+measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
+measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
+measure_values--nepFC_PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
+measure_values--nepFC_K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
+measure_values--nepFC_SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
+baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
+baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y
diff --git a/data/meta_nepExplorer.rda b/data/meta_nepExplorer.rda