Task 2

.Rbuildignore

@@ -3,3 +3,7 @@
 _\.new\.png$
 ^\.positai$
 ^\.claude$
+^plans$
+MSstats_log_.*\.log$
+^[^/]*\.csv$
+^\.github$

.gitignore

@@ -52,3 +52,6 @@ vignettes/*.pdf
 
 /*.csv
 .positai
+
+# Local planning docs (not part of the package)
+plans/

NAMESPACE

@@ -210,6 +210,7 @@ importFrom(stats,hclust)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,qt)
+importFrom(stats,setNames)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_extract_all)

R/constants.R

@@ -188,7 +188,19 @@ NAMESPACE_QC = list(
   ptm_downloads_panel = "ptm_downloads_panel",
   # Data Upload tab template-gated upload panels
   data_upload_mapping_panel = "data_upload_mapping_panel",
-  data_upload_ratios_panel = "data_upload_ratios_panel"
+  data_upload_ratios_panel = "data_upload_ratios_panel",
+  tracer_constants_panel = "tracer_constants_panel",
+  tracer_constants_file = "tracer_constants_file",
+  tracer_constants_clear = "tracer_constants_clear",
+  tracer_constants_status = "tracer_constants_status"
+)
+
+CONSTANTS_QC = list(
+  tracer_min = 0.01,
+  tracer_max = 1,
+  tracer_source_upload = "upload",
+  tracer_source_none = "none",
+  tracer_source_not_run = "not_run"
 )
 
 NAMESPACE_EXPDES = list(

R/module-qc-server.R

@@ -9,8 +9,14 @@
 #' @param parent_session session of the main calling module
 #' @param loadpage_input input object from loadpage UI
 #' @param get_data stored function that returns the data from loadpage
+#' @param app_template reactive (or NULL) returning the selected template name (e.g. TEMPLATES$default)
+#' @param get_condition_metadata reactive (or NULL) returning the condition metadata table
 #'
-#' @return input object with user selected options
+#' @return a list with four elements: `input` (the module's input object),
+#'   `preprocessData` (reactive returning the preprocessed data),
+#'   `turnoverRatios` (reactive returning the turnover ratios, or the uploaded
+#'   ratios when those override them), and `tracerConstants` (reactive
+#'   returning the tracer-constant provenance record snapshotted at Run)
 #'
 #' @export
 #' @examples
@@ -25,12 +31,13 @@ qcServer <- function(input, output, session, parent_session, loadpage_input, get
     preprocessData(input, loadpage_input(), get_data())
   })
 
-  turnover_ratios <- register_qc_turnover(input, output, session, app_template, get_data,
-                                          get_condition_metadata, preprocess_data)
+  turnover = register_qc_turnover(input, output, session, app_template, get_data,
+                                  get_condition_metadata, preprocess_data)
 
   data_upload = register_qc_data_upload(input, output, session, loadpage_input,
                                         app_template, get_data, preprocess_data,
-                                        get_condition_metadata, turnover_ratios)
+                                        get_condition_metadata, turnover$ratios,
+                                        turnover$tracer_upload)
 
   effective_preprocess_data <- data_upload$effective_preprocess_data
 
@@ -97,7 +104,8 @@ qcServer <- function(input, output, session, parent_session, loadpage_input, get
     list(
       input = input,
       preprocessData = effective_preprocess_data,
-      turnoverRatios = data_upload$effective_turnover_ratios
+      turnoverRatios = data_upload$effective_turnover_ratios,
+      tracerConstants = turnover$tracer_constants
     )
   )
 }

R/module-qc-ui.R

@@ -186,8 +186,37 @@ qcUI <- function(id) {
 
         )),
 
-        tags$hr(),
-        uiOutput(ns("tracer_constants_sidebar")),
+        # Tracer constants (protein turnover only), toggled server-side by
+        # register_qc_turnover.
+        shinyjs::hidden(div(
+          id = ns(NAMESPACE_QC$tracer_constants_panel),
+          tags$hr(),
+          h4("Tracer constants", class = "icon-wrapper",
+             icon("question-circle", lib = "font-awesome"),
+             div(paste0(
+               "Optional: corrects each condition's heavy fraction for ",
+               "incomplete label enrichment by dividing it by this constant ",
+               "(1 = no correction; leave empty to use 1 everywhere). ",
+               "Upload a CSV with columns ",
+               paste(get_qc_required_tracer_columns(), collapse = ", "),
+               " (case-sensitive), one row per condition -- GROUP must match ",
+               "your experimental condition names exactly, including case. ",
+               "TracerConstant must be between ", CONSTANTS_QC$tracer_min,
+               " and ", CONSTANTS_QC$tracer_max, ". Example: header ",
+               "'GROUP,TracerConstant', then '0h,0.98', '6h,0.95', ",
+               "'24h,0.93'. Condition names must start with a number of ",
+               "hours (d or w for days/weeks); names the app can't parse, ",
+               "or that duplicate a timepoint, are rejected."),
+               class = "icon-tooltip")),
+          fileInput(ns(NAMESPACE_QC$tracer_constants_file),
+                    "Upload tracer constants (CSV)", accept = ".csv"),
+          p(tags$strong("Required columns: "),
+            paste(get_qc_required_tracer_columns(), collapse = ", ")),
+          actionButton(ns(NAMESPACE_QC$tracer_constants_clear), "Clear",
+                       class = "btn-sm"),
+          tags$br(), tags$br(),
+          uiOutput(ns(NAMESPACE_QC$tracer_constants_status))
+        )),
         actionButton(ns("run"), "Run summarization"),
         width = 3
       ),
@@ -230,7 +259,8 @@ qcUI <- function(id) {
                               id = ns(NAMESPACE_QC$data_upload_ratios_panel),
                               tags$hr(),
                               fileInput(ns("upload_turnover_ratios"), "Upload Turnover Ratios (CSV)", accept = ".csv"),
-                              p(tags$strong("Required columns: "), "Protein, TimeVal, H_frac, L_frac")
+                              p(tags$strong("Required columns: "), "Protein, TimeVal, H_frac, L_frac"),
+                              p("Ratios uploaded here are used as given. The tracer-constants upload in the side panel does not apply on this flow: these H_frac and L_frac values are already computed, so any correction for incomplete label enrichment must be applied before upload.")
                             ))
                           )
                  ),

R/module-statmodel-server.R

@@ -14,6 +14,11 @@
 #' @param get_data stored function that returns the data from loadpage
 #' @param preprocess_data stored function that returns preprocessed data
 #' @param app_template reactive returning the selected template name (e.g. TEMPLATES$default)
+#' @param turnover_ratios reactive returning the calculated turnover ratios
+#' @param condition_metadata reactive returning the condition metadata table
+#' @param tracer_constants reactive returning the tracer-constant provenance
+#'   record snapshotted by the QC page at Run (values / source / file), or
+#'   NULL when the data-processing page has not been run in this session
 #'
 #' @importFrom MSstatsResponse visualizeResponseProtein
 #'
@@ -27,7 +32,8 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
                            get_data, preprocess_data,
                            app_template = reactive(TEMPLATES$default),
                            turnover_ratios = reactive(NULL),
-                           condition_metadata = reactive(NULL)) {
+                           condition_metadata = reactive(NULL),
+                           tracer_constants = reactive(NULL)) {
   moduleServer(
     id,
     function(input, output, session) {
@@ -394,7 +400,9 @@ statmodelServer = function(id, parent_session, loadpage_input, qc_input,
       data_comparison_code = eventReactive(input[[NAMESPACE_STATMODEL$modeling_start]], {
         req(contrast$matrix)
         comp_mat = contrast$matrix
-        generate_analysis_code(qc_input(), loadpage_input(), comp_mat, input, app_template())
+        tracer_used = tryCatch(tracer_constants(), error = function(e) NULL)
+        generate_analysis_code(qc_input(), loadpage_input(), comp_mat, input,
+                               app_template(), tracer_used)
       })
 
       SignificantProteins = eventReactive(input[[NAMESPACE_STATMODEL$modeling_start]], {