From efc0804b456265952c6091b838ef316522d84623 Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Fri, 8 Jul 2022 13:02:02 +0200
Subject: [PATCH] Threshold es defineix pel 50% dels pics. Es pot modificar a
 posteriori.

---
 chromatoR/app.R | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/chromatoR/app.R b/chromatoR/app.R
index a3479a6..7d04f99 100644
--- a/chromatoR/app.R
+++ b/chromatoR/app.R
@@ -14,7 +14,8 @@ ui <- fluidPage(
         tabPanel("Detección de Bases",
           sidebarPanel(
             fileInput("file1", "Sube fichero ab1", multiple = FALSE),
-            numericInput("thr", label = "Peak Threshold", value = 450),
+            # numericInput("thr", label = "Peak Threshold", value = 450),
+            uiOutput('thr'),
             numericInput("dist1", label = "1st Distance Reduction", value = 4),
             numericInput("dist2", label = "2nd Distance Reduction", value = 7),
             numericInput("ratio", label = "Ratio 2ary seq", value = 0.33),
@@ -60,6 +61,31 @@ server <- function(input, output) {
     }
   })
   
+  output$thr<-renderUI({
+    if (!is.null(obj$aborig)){
+      print(1)
+      obj_ab<-obj$aborig
+      ## Functions
+      getpeaks <- function(trace) {
+        r <- rle(trace)
+        indexes <- which(rep(diff(sign(diff(c(-Inf, r$values, -Inf)))) == -2,
+                             times = r$lengths))
+        cbind(indexes, trace[indexes])
+      }
+      
+      Apeaks <- getpeaks(obj_ab@traceMatrix[,1])
+      Cpeaks <- getpeaks(obj_ab@traceMatrix[,2])
+      Gpeaks <- getpeaks(obj_ab@traceMatrix[,3])
+      Tpeaks <- getpeaks(obj_ab@traceMatrix[,4])
+      
+      peakCusMatrix<-rbind(Gpeaks, 
+                           Apeaks, 
+                           Tpeaks, 
+                           Cpeaks)
+      thr_calc<-quantile(peakCusMatrix[,2], 0.5)
+      numericInput("thr", label = "Peak Threshold", value = thr_calc)
+    }
+  })
   
   observeEvent(input$calab, {
     if (!is.null(obj$aborig)){