From 5680ced129b1188368d800b60cffc1096dcd03dc Mon Sep 17 00:00:00 2001
From: weaversd <sweaver4@nd.edu>
Date: Tue, 30 Jul 2024 20:25:01 -0400
Subject: [PATCH] bug fixes with DIANN import sample count

---
 Documentation/Release Updates.txt | 6 +++++-
 ui.R                              | 2 +-
 www/basic_functions.R             | 3 ++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/Documentation/Release Updates.txt b/Documentation/Release Updates.txt
index 300b638..bc4501d 100644
--- a/Documentation/Release Updates.txt	
+++ b/Documentation/Release Updates.txt	
@@ -65,4 +65,8 @@ Version 0.1.13
   
 Version 0.1.14
 2024-02-22
-  - Bug fixed for importing peaks files
\ No newline at end of file
+  - Bug fixed for importing peaks files
+  
+Version 0.1.15
+2024-07-30
+  - Bug fixed for importing DIANN files where the sample count was calculated improperly when filtering based on Regex.
\ No newline at end of file
diff --git a/ui.R b/ui.R
index 8fb7caa..f4fcc25 100644
--- a/ui.R
+++ b/ui.R
@@ -2,7 +2,7 @@ library(shiny)
 ui <- navbarPage(title = "PrIntMap-R",
                  tabPanel("Documentation",
                           includeMarkdown("Documentation/Documentation.md"),
-                          "Version 0.1.14"), #update version here for each push
+                          "Version 0.1.15"), #update version here for each push
                  tabPanel("Run",
                           flowLayout(
                             fileInput(inputId = "database_file", label = "Upload fasta database file",
diff --git a/www/basic_functions.R b/www/basic_functions.R
index 2de4f9e..cd3cb87 100644
--- a/www/basic_functions.R
+++ b/www/basic_functions.R
@@ -531,7 +531,7 @@ read_peptide_tsv_DIANN_comb <- function(peptide_file, sample_pattern, sample = N
       names(peptides)[grepl("Stripped.Sequence", names(peptides))] <- "sequence"
       names(peptides)[grepl("Precursor.Quantity", names(peptides))] <- "Intensity"
       
-      sample_count <- length(unique(peptide_import$File.Name))
+      sample_count <- length(unique(peptides$File.Name))
       if (comb_method=="Average"){
         peptides$Intensity <- peptides$Intensity / sample_count
       }
@@ -549,6 +549,7 @@ read_peptide_tsv_DIANN_comb <- function(peptide_file, sample_pattern, sample = N
     }
   } else{
     if (sample_pattern != ""){
+      peptides <- peptide_import
       if(length(names(peptides)[grepl(sample_pattern, names(peptides))])<=0){
         stop("Sample Pattern not found in file.")
       } else {