Merge pull request #151 from OHDSI/add_impute_missings

Add impute missings option in the shiny
OHDSI · Dec 4, 2024 · 4e393f4 · 4e393f4
2 parents 20fca6f + da706db
commit 4e393f4
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Showing 4 changed files with 21 additions and 5 deletions.
diff --git a/inst/shiny/global.R b/inst/shiny/global.R
@@ -39,8 +39,9 @@ if(file.exists(here::here("data", "appData.RData"))){
   cli::cli_alert_success("Data processed")
 }
 
-plotComparedLsc <- function(lsc, cohorts, colour = NULL, facet = NULL){
+plotComparedLsc <- function(lsc, cohorts, imputeMissings, colour = NULL, facet = NULL){
    lsc <- lsc |>  tidy()
+
   plot_data <- lsc |>
     filter(cohort_name %in% c(cohorts
     )) |>
@@ -54,6 +55,11 @@ plotComparedLsc <- function(lsc, cohorts, colour = NULL, facet = NULL){
     pivot_wider(names_from = cohort_name,
                 values_from = percentage)
 
+  if(isTRUE(imputeMissings)){
+    plot_data <- plot_data |> 
+      mutate(across(c(cohorts[1], cohorts[2]), ~if_else(is.na(.x), 0, .x)))
+  }
+
     plot <- plot_data |>
     ggplot(aes(text = paste("<br>Database:", database,
                             "<br>Concept:", variable_name,

diff --git a/inst/shiny/scripts/preprocess.R b/inst/shiny/scripts/preprocess.R
@@ -98,7 +98,7 @@ selected$compare_large_scale_characteristics_grouping_domain <- choices$compare_
 if(!is.null(dataFiltered$summarise_large_scale_characteristics)){
   if(nrow(dataFiltered$summarise_large_scale_characteristics)>0){
     choices$summarise_large_scale_characteristics_grouping_domain <- settings(dataFiltered$summarise_large_scale_characteristics) |>
-      pull("table_name")
+      pull("table_name") |> unique()
     selected$summarise_large_scale_characteristics_grouping_domain <- choices$summarise_large_scale_characteristics_grouping_domain
   }}
 

diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -1074,7 +1074,7 @@ server <- function(input, output, session) {
 
   output$gt_compare_lsc <- DT::renderDT({
     lscFiltered <- outputLSC()
-    
+
     if (nrow(lscFiltered) == 0) {
       validate("No results found for selected inputs")
     }
@@ -1095,6 +1095,11 @@ server <- function(input, output, session) {
       pivot_wider(names_from = cohort_name,
                   values_from = percentage)
 
+    if(isTRUE(input$compare_large_scale_characteristics_impute_missings)){
+      lsc <- lsc |> 
+        mutate(across(c(target_cohort, comparator_cohort), ~if_else(is.na(.x), 0, .x)))
+    }
+
     lsc <-lsc |>
       mutate(across(c(target_cohort, comparator_cohort), ~ as.numeric(.x)/100)) |>
       mutate(smd = (!!sym(target_cohort) - !!sym(comparator_cohort))/sqrt((!!sym(target_cohort)*(1-!!sym(target_cohort)) + !!sym(comparator_cohort)*(1-!!sym(comparator_cohort)))/2)) |>
@@ -1128,7 +1133,8 @@ server <- function(input, output, session) {
                     cohorts = c(input$compare_large_scale_characteristics_grouping_cohort_1,
                                 input$compare_large_scale_characteristics_grouping_cohort_2),
                     colour = c(input$compare_large_scale_characteristics_colour_1),
-                    facet  = c(input$compare_large_scale_characteristics_facet_1)
+                    facet  = c(input$compare_large_scale_characteristics_facet_1),
+                    imputeMissings = input$compare_large_scale_characteristics_impute_missings
     )
   })
 

diff --git a/inst/shiny/ui.R b/inst/shiny/ui.R
@@ -662,7 +662,11 @@ ui <- bslib::page_navbar(
                                          selected = NULL,
                                          multiple = TRUE,
                                          options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3")
-                                       )
+                                       ),
+                                       shinyWidgets::prettyCheckbox(
+                                         inputId = "compare_large_scale_characteristics_impute_missings",
+                                         label = "Impute missing values as 0",
+                                         value = FALSE)
                                      )
                                    )
         ),