From bac2a2920011f3369ffb562c0094933867fb6b52 Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@protonmail.com>
Date: Fri, 13 Nov 2020 20:03:51 +0100
Subject: [PATCH] Correct 'cuttofs'

---
 invivos/app.R | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/invivos/app.R b/invivos/app.R
index bb0ee06..1fbded3 100644
--- a/invivos/app.R
+++ b/invivos/app.R
@@ -244,8 +244,7 @@ server <- function(input, output) {
       observeEvent(analysis$taula, {})
       stattest<-"dunn"
       oneside<-""
-      cutoff<-750
-      
+
       table<-analysis$taula
       if ("ID.animal" %in% colnames(table)){table<-rename(table, "ID animal"=`ID.animal`)}
       if ("ID" %in% colnames(table)){table<-rename(table, "ID animal"=ID)}
@@ -339,7 +338,7 @@ server <- function(input, output) {
         g<-list()
         for (side in c("L","R")){
           tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
-          endtime<-dcast(tableR %>% filter(Volume < cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+          endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
           endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
           table_tumor<<-endtime
           
@@ -363,7 +362,7 @@ server <- function(input, output) {
         
       }else{
         tableR<-table %>% filter(!is.na(Volume))
-        endtime<-dcast(tableR %>% filter(Volume < cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+        endtime<-dcast(tableR %>% filter(Volume < input$cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
         endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
         table_tumor<<-endtime
         
@@ -381,7 +380,6 @@ server <- function(input, output) {
   output$stats<-renderPrint({
     stattest<-"dunn"
     oneside<-""
-    cutoff<-750
     if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
       observeEvent(analysis$taula_def, {})
       table<-analysis$taula_def
@@ -403,7 +401,6 @@ server <- function(input, output) {
   output$tab_stats<-renderTable({
     stattest<-"dunn"
     oneside<-""
-    cutoff<-750
     if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
       table<-analysis$taula_def
       table_stats<-list()
@@ -519,7 +516,7 @@ server <- function(input, output) {
           count<-1
           for (side in c("L","R")){
             tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
-            endtime<-dcast(tableR %>% filter(Volume < cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+            endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
             endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
             table_tumor<-endtime
             if (input$colors != ""){
@@ -540,7 +537,7 @@ server <- function(input, output) {
           
         }else{
           tableR<-table %>% filter(!is.na(Volume))
-          endtime<-dcast(tableR %>% filter(Volume < cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+          endtime<-dcast(tableR %>% filter(Volume < input$cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
           endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
           table_tumor<-endtime
           if (input$colors != ""){