Add ptms

server.R

@@ -7,6 +7,30 @@ options(shiny.maxRequestSize=100*1024^2)
 
 server <- function(input, output, session) {
 
+
+  ptm_data <- reactive({
+    # Check if user uploaded a file
+    if (!is.null(input$custom_ptm_file)) {
+      file_path <- input$custom_ptm_file$datapath  # Path of uploaded file
+    } else {
+      file_path <- "www/ptm_list.csv"  # Default file
+    }
+
+    # Read CSV and return as dataframe
+    read.csv(file_path, stringsAsFactors = FALSE)
+  })
+
+  # Render dynamic UI based on the selected PTM file
+  output$ptm_selection <- renderUI({
+    tipify(
+      checkboxGroupInput(inputId = "PTM",
+                         label = "PTMs",
+                         choiceNames = ptm_data()$Choice,  # Display names from CSV
+                         choiceValues = ptm_data()$Value   # Corresponding values
+      ), "Select one or more PTMs to annotate"
+    )
+  })
+
   database <- reactive({
     validate(
       need(!is.null(input$database_file), "No Database File Provided")

ui.R

@@ -71,26 +71,17 @@ ui <- navbarPage(title = "PrIntMap-R",
                                 fluidRow(
                                   checkboxInput(inputId = "displayPTMs",
                                                 label = "Display PTMs"),
-                                  tipify(checkboxGroupInput(inputId = "PTM",
-                                                            label = "PTMs",
-                                                            choiceNames = c("Carbamidomethylation",
-                                                                            "Deamidation",
-                                                                            "Oxidation" ,
-                                                                            "Pyro_glu_from_E" ,
-                                                                            "Pyro_glu_from_Q",
-                                                                            "Sodium_adduct"
-                                                            ),
-                                                            choiceValues = c("(+57.02)",
-                                                                             "(+0.98)",
-                                                                             "(+15.99)",
-                                                                             "(-18.01)",
-                                                                             "(-17.03)",
-                                                                             "(+21.98)"
-                                                            )), "Select one or more PTMs to annotate"),
+                                  fileInput(inputId = "custom_ptm_file", 
+                                            label = "Upload Custom PTM CSV", 
+                                            accept = c(".csv")),
+                                  uiOutput("ptm_selection"),  # Dynamically generated UI
                                   checkboxInput(inputId = "custom_PTM_check",
-                                                label = "CUSTOM", value = F),
+                                                label = "CUSTOM", value = FALSE),
                                   tipify(textInput(inputId = "custom_PTM",
-                                                   label = "Custom PTM"), "Enter a custom PTM (CUSTOM checkbox must be selected. Enter the PTM as a string as it is seen in the peptide column of your sample input."),))
+                                                   label = "Custom PTM"), 
+                                         "Enter a custom PTM (CUSTOM checkbox must be selected. Enter the PTM as a string as it is seen in the peptide column of your sample input."),    
+                                )
+                              )
                             ),
                             tipify(checkboxInput(inputId = "disp_origin",
                                                  label = "Display Origin Peptides",

www/basic_functions.R

@@ -706,18 +706,22 @@ create_peptide_origin_vec <- function(peptide_df,
   vector_list <- list()
   for (i in 1:nrow(peptide_df)) {
     peptide <- peptide_df$sequence[i]
+    modpeptide <- peptide_df$Peptide[i]
     intensity_value <- peptide_df[[intensity]][i]
     matches_df <- str_locate_all(protein, peptide)[[1]]
     matches_count <- nrow(matches_df)
     origin_vector <- rep("", nchar(protein))
+    mod_origin_vector <- rep("", nchar(protein))
     if (matches_count > 0) {
       for (j in 1:matches_count) {
         start <- matches_df[[j,1]]
         end <- matches_df[[j,2]]
         origin_vector[start:end] <- paste0(peptide, "|")
+        mod_origin_vector[start:end] <- paste0(modpeptide, "|")
       }
     }
     vector_list[[i]] <- origin_vector
+    vector_list[[i]] <- mod_origin_vector
   }
   origin_df <- as.data.frame(sapply(vector_list, unlist))
   origin_vec <- apply(origin_df, 1, paste, collapse="")

www/ptm_list.csv

@@ -0,0 +1,10 @@
+Choice,Value
+Carbamidomethylation,(+57.02)
+Deamidation,(+0.98)
+Oxidation,(+15.99)
+Pyro_glu_from_E,(-18.01)
+Pyro_glu_from_Q,(-17.03)
+Sodium_adduct,(+21.98)
+Acetylation,(+42.0106)
+iTRAQ 4-plex,(+229.1629)
+TMT 10-plex,(+144.1021)