From 9f4fbe4619867061e85c22a5d709df4972f30ec7 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 29 Jan 2026 15:15:56 -0500
Subject: [PATCH] feat(doseResponseFit): Add progress bar

---
 DESCRIPTION                                                   | 3 ++-
 NAMESPACE                                                     | 2 ++
 R/Fit_Isotonic_Regression.R                                   | 4 ++++
 ...vertGroupToNumericDose.Rd => convertGroupToNumericDose.Rd} | 0
 man/{DoseResponseFit.Rd => doseResponseFit.Rd}                | 2 +-
 ...eExperimentSimulation.Rd => futureExperimentSimulation.Rd} | 0
 man/{PredictIC50Parallel.Rd => predictIC50Parallel.Rd}        | 0
 ...isualizeResponseProtein.Rd => visualizeResponseProtein.Rd} | 0
 8 files changed, 9 insertions(+), 2 deletions(-)
 rename man/{ConvertGroupToNumericDose.Rd => convertGroupToNumericDose.Rd} (100%)
 rename man/{DoseResponseFit.Rd => doseResponseFit.Rd} (96%)
 rename man/{FutureExperimentSimulation.Rd => futureExperimentSimulation.Rd} (100%)
 rename man/{PredictIC50Parallel.Rd => predictIC50Parallel.Rd} (100%)
 rename man/{VisualizeResponseProtein.Rd => visualizeResponseProtein.Rd} (100%)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0e40607..2f27d1b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,7 +31,8 @@ Imports:
     dplyr,
     stats,
     parallel,
-    data.table
+    data.table,
+    utils
 Suggests:
     MSstats,
     MSstatsTMT,
diff --git a/NAMESPACE b/NAMESPACE
index d7a1451..d40cab3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,3 +48,5 @@ importFrom(stats,pf)
 importFrom(stats,quantile)
 importFrom(stats,rlnorm)
 importFrom(stats,rnorm)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)
diff --git a/R/Fit_Isotonic_Regression.R b/R/Fit_Isotonic_Regression.R
index 48724f5..0c5cb6e 100644
--- a/R/Fit_Isotonic_Regression.R
+++ b/R/Fit_Isotonic_Regression.R
@@ -64,6 +64,7 @@
 #' @importFrom stats pf p.adjust
 #' @importFrom dplyr filter select mutate group_by summarise arrange distinct
 #' @importFrom data.table rbindlist
+#' @importFrom utils setTxtProgressBar txtProgressBar
 doseResponseFit = function(data, weights = NULL,
                            increasing = FALSE,
                            transform_dose = TRUE,
@@ -92,6 +93,7 @@ doseResponseFit = function(data, weights = NULL,
     protein_list = unique(drug_subset$protein)
     results_list = list()
 
+    progress_bar = txtProgressBar(min = 0, max = length(protein_list), style = 3)
     for (i in seq_along(protein_list)) {
       tryCatch({
         suppressWarnings({
@@ -130,11 +132,13 @@ doseResponseFit = function(data, weights = NULL,
           results_temp$drug = drug_type
           results_temp = results_temp[, c("protein", "drug", setdiff(names(results_temp), c("protein", "drug")))]
           results_list[[i]] = results_temp
+          setTxtProgressBar(progress_bar, i)
         })
       }, error = function(e) {
         warning(paste("Error for drug:", drug_type, "protein:", protein_list[i], ":", conditionMessage(e)))
       })
     }
+    close(progress_bar)
 
     # Combine and adjust p-values for this drug
     if (length(results_list) > 0) {
diff --git a/man/ConvertGroupToNumericDose.Rd b/man/convertGroupToNumericDose.Rd
similarity index 100%
rename from man/ConvertGroupToNumericDose.Rd
rename to man/convertGroupToNumericDose.Rd
diff --git a/man/DoseResponseFit.Rd b/man/doseResponseFit.Rd
similarity index 96%
rename from man/DoseResponseFit.Rd
rename to man/doseResponseFit.Rd
index 07dd21f..3033264 100644
--- a/man/DoseResponseFit.Rd
+++ b/man/doseResponseFit.Rd
@@ -66,7 +66,7 @@ interaction_results <- doseResponseFit(
 print(interaction_results)
 
 # Check significant interactions
-significant <- interaction_results[interaction_results$adjust_pval < 0.05, ]
+significant <- interaction_results[interaction_results$adj.pvalue < 0.05, ]
 print(paste("Found", nrow(significant), "significant interactions"))
 
 \dontrun{
diff --git a/man/FutureExperimentSimulation.Rd b/man/futureExperimentSimulation.Rd
similarity index 100%
rename from man/FutureExperimentSimulation.Rd
rename to man/futureExperimentSimulation.Rd
diff --git a/man/PredictIC50Parallel.Rd b/man/predictIC50Parallel.Rd
similarity index 100%
rename from man/PredictIC50Parallel.Rd
rename to man/predictIC50Parallel.Rd
diff --git a/man/VisualizeResponseProtein.Rd b/man/visualizeResponseProtein.Rd
similarity index 100%
rename from man/VisualizeResponseProtein.Rd
rename to man/visualizeResponseProtein.Rd