clean and lint

pharmaverse · Jan 20, 2025 · bc66f5c · bc66f5c
1 parent 686095c
commit bc66f5c
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Showing 7 changed files with 44 additions and 25 deletions.
diff --git a/R/format_data.R b/R/format_data.R
@@ -97,7 +97,7 @@ format_pkncadose_data <- function(pkncaconc_data,
     slice(1) %>%
     ungroup() %>%
     arrange(!!!syms(group_columns))
-  
+
 }
 
 #' Create Dose Intervals Dataset

diff --git a/R/general_lineplot.R b/R/general_lineplot.R
@@ -52,7 +52,8 @@
 #' @importFrom tern g_ipp
 #' @export
 general_lineplot <- function(
-  data, selected_analytes, selected_pcspec, selected_usubjids, colorby_var, time_scale, yaxis_scale, cycle = NULL
+  data, selected_analytes, selected_pcspec, selected_usubjids,
+  colorby_var, time_scale, yaxis_scale, cycle = NULL
 ) {
 
   # Check if the data is empty
@@ -75,6 +76,10 @@ general_lineplot <- function(
       DOSEA = factor(DOSEA),
       id_var = interaction(!!!syms(colorby_var), sep = ", ")
     )
+  # Check if the data is empty
+  if (nrow(preprocessed_data) == 0) {
+    return(ggplot() + ggtitle("No data available for selected parameters"))
+  }
 
   # If there are predose records duplicate them in the previous line so they are considered
   if ("ARRLT" %in% names(preprocessed_data) &&

diff --git a/R/lambda_slope_plot.R b/R/lambda_slope_plot.R
@@ -63,7 +63,8 @@ lambda_slope_plot <- function(
 
   # Obtain all information relevant regarding lambda calculation
   lambda_res <- res_pknca_df %>%
-    filter(DOSNO == dosno, USUBJID == usubjid, ANALYTE == analyte, PCSPEC == pcspec, type_interval == "main")  %>%
+    filter(DOSNO == dosno, USUBJID == usubjid, ANALYTE == analyte,
+           PCSPEC == pcspec, type_interval == "main")  %>%
     arrange(USUBJID, DOSNO, ANALYTE, PCSPEC, start, desc(end)) %>%
     filter(!duplicated(paste0(USUBJID, DOSNO, PCSPEC, ANALYTE, PPTESTCD)))
 
@@ -236,7 +237,7 @@ lambda_slope_plot <- function(
   pl <- pl %>%
     # Make this trace the only one
     add_trace(
-      data = plot_data %>% filter(DOSNO == dosno, USUBJID == usubjid, 
+      data = plot_data %>% filter(DOSNO == dosno, USUBJID == usubjid,
                                   ANALYTE == analyte, PCSPEC == pcspec),
       x = ~TIME, y = ~log10(AVAL),
       customdata = ~paste0(USUBJID, "_", DOSNO, "_", IX),

diff --git a/inst/shiny/modules/slope_selector.R b/inst/shiny/modules/slope_selector.R
@@ -95,7 +95,9 @@ slope_selector_ui <- function(id) {
 .SLOPE_SELECTOR_COLUMNS <- c("TYPE", "PATIENT", "ANALYTE", "PCSPEC", "PROFILE", "IXrange", "REASON")
 
 slope_selector_server <- function(
-  id, mydata, res_nca, profiles_per_patient, cycle_nca, analyte_nca, pcspec_nca, pk_nca_trigger, settings_upload
+  id, mydata, res_nca, profiles_per_patient,
+  cycle_nca, analyte_nca, pcspec_nca,
+  pk_nca_trigger, settings_upload
 ) {
   moduleServer(id, function(input, output, session) {
     log_trace("{id}: Attaching server")
@@ -402,7 +404,11 @@ slope_selector_server <- function(
       shiny::debounce(750)
 
     # Define the click events for the point exclusion and selection in the slope plots
-    last_click_data <- reactiveValues(patient = "", profile = "", analyte = "", pcspec =  "", idx_pnt = "")
+    last_click_data <- reactiveValues(
+      patient = "", profile = "",
+      analyte = "", pcspec =  "",
+      idx_pnt = ""
+    )
     observeEvent(event_data("plotly_click", priority = "event"), {
       # Store the information of the last click event #
       click_data <- event_data("plotly_click")

diff --git a/inst/shiny/modules/tab_visuals.R b/inst/shiny/modules/tab_visuals.R
@@ -128,7 +128,7 @@ tab_visuals_ui <- function(id) {
           orderInput(
             ns("summary_groupby"),
             "..to hierarchically group by (order matters!):",
-            items = c( "ANALYTE", "PCSPEC", "DOSNO"),
+            items = c("ANALYTE", "PCSPEC", "DOSNO"),
             width = shiny::validateCssUnit("100%"),
             connect = ns("summary_groupby_source"),
             placeholder = "Drag items here to group hierarchically..."
@@ -223,13 +223,14 @@ tab_visuals_server <- function(id, data, grouping_vars, res_nca) {
       param_choices_pcspec <- data() %>%
         pull(PCSPEC) %>%
         unique()
-      
+
       updatePickerInput(
         session,
         "generalplot_pcspec",
         choices = param_choices_pcspec,
+        selected = param_choices_pcspec[1]
       )
-      
+
       # Update the usubjid picker input
       param_choices_usubjid <- data() %>%
         pull(USUBJID) %>%
@@ -244,7 +245,7 @@ tab_visuals_server <- function(id, data, grouping_vars, res_nca) {
 
       # Update the colorby picker input
       param_choices_colorby <- sort(
-        c("STUDYID", "PCSPEC", "ANALYTE", "DOSEA", "DOSNO", "USUBJID", grouping_vars()) 
+        c("STUDYID", "PCSPEC", "ANALYTE", "DOSEA", "DOSNO", "USUBJID", grouping_vars())
       )
 
       updatePickerInput(
@@ -262,7 +263,8 @@ tab_visuals_server <- function(id, data, grouping_vars, res_nca) {
       updateSelectInput(
         session,
         "analyte_mean",
-        choices = sort(analyte_choices)
+        choices = sort(analyte_choices),
+        selected = analyte_choices[1]
       )
 
       # Update the studyidmean select input
@@ -275,20 +277,21 @@ tab_visuals_server <- function(id, data, grouping_vars, res_nca) {
         "studyid_mean",
         choices = sort(studyid_choices)
       )
-      
+
       # Update pcspec mean choices
       pcspec_choices <- data() %>%
         pull(PCSPEC) %>%
         unique()
-      
+
       updateSelectInput(
         session,
         "pcspec_mean",
-        choices = sort(pcspec_choices)
+        choices = sort(pcspec_choices),
+        selected = pcspec_choices[1]
       )
 
       # Update the selectidvar select input
-      idvar_choices <- c("ANALYTE","PCSPEC", "DOSEA", grouping_vars())
+      idvar_choices <- c("ANALYTE", "PCSPEC", "DOSEA", grouping_vars())
 
       updateSelectInput(
         session,

diff --git a/inst/shiny/tabs/nca.R b/inst/shiny/tabs/nca.R
@@ -19,7 +19,8 @@ observeEvent(data(), {
     session,
     inputId = "select_analyte",
     label = "Choose the Analyte(s) :",
-    choices = unique(data()$ANALYTE)
+    choices = unique(data()$ANALYTE),
+    selected = unique(data()$ANALYTE)[1]
   )
 })
 
@@ -28,7 +29,8 @@ observeEvent(data(), {
     session,
     inputId = "select_pcspec",
     label = "Choose the Specimen Type(s) :",
-    choices = unique(data()$PCSPEC)
+    choices = unique(data()$PCSPEC),
+    selected = unique(data()$PCSPEC)[1]
   )
 })
 
@@ -481,7 +483,7 @@ res_nca <- eventReactive(pk_nca_trigger(), {
     myres$result <- myres$result %>%
       inner_join(select(mydata()$dose$data, -exclude)) %>%
       mutate(start = start - !!sym(mydata()$dose$columns$time),
-                    end = end - !!sym(mydata()$dose$columns$time)) %>%
+             end = end - !!sym(mydata()$dose$columns$time)) %>%
       select(names(myres$result))
 
     # Return the result

diff --git a/inst/shiny/ui.R b/inst/shiny/ui.R
@@ -51,20 +51,22 @@ fluidPage(
                 # Selection of analyte
                 selectInput(
                   "select_analyte",
-                  "Choose the Analyte :",
-                  choices = NULL,
-                  multiple = TRUE),
+                  "Choose the Analyte(s) :",
+                  choices = c("Please specify ANALYTE" = ""),
+                  multiple = TRUE
+                ),
                 # Selection of matrix
                 selectInput(
                   "select_pcspec",
-                  "Choose the Matrix:",
-                  choices = NULL,
-                  multiple = TRUE),
+                  "Choose the Specimen Type(s):",
+                  choices = c("Please specify PCSPEC" = ""),
+                  multiple = TRUE
+                ),
                 selectInput(
                   "select_dosno",
                   "Choose the Dose Number:",
                   multiple = TRUE,
-                  choices = c("Please specify ANALYTE in Data Selection" = "")
+                  choices = c("Please specify ANALYTE first" = "")
                 ),
                 br(),
                 actionButton("submit_analyte", "Submit"),