From e481ee411c2be2a2a68de3073a8150115c7e248f Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Fri, 10 Feb 2023 14:26:17 +0100
Subject: [PATCH] Cambiar Supervivencia y Kluskal de formato.

---
 invivos/app.R | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/invivos/app.R b/invivos/app.R
index 4b5836f..c17631e 100755
--- a/invivos/app.R
+++ b/invivos/app.R
@@ -493,15 +493,15 @@ server <- function(input, output) {
   })
   
   output$survival<-renderPlot({
-    if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
-      observeEvent(analysis$taula_def, {})
-      table<-analysis$taula_def
+    if (!is.null(input$file_analy) & !is.null(analysis$taula)){
+      observeEvent(analysis$taula, {})
+      table<-analysis$taula
       if (input$vacc == "Sí"){
         g<-list()
         for (side in c("L","R")){
-          tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
-          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
+          tableR<-filter(table, Side == side) %>% filter(!is.na(Volume))
+          endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Cage+Animal+Side+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+          endtime["Dead"]<-dcast(tableR, Cage+Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
           table_tumor<<-endtime
           
           g[side]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor),
@@ -524,9 +524,9 @@ server <- function(input, output) {
         
       }else{
         tableR<-table %>% filter(!is.na(Volume))
-        endtime<-dcast(if(length(unique(tableR$Timepoint)) > 1){tableR %>% filter(Volume < input$cutoff)}else{tableR}, `ID animal`+`ID tumor`+Group~., 
-                       value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
-        endtime["Dead"]<-dcast(tableR, `ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") >= input$cutoff
+        endtime<-dcast(if(length(unique(tableR$DayPostInoc)) > 1){tableR %>% filter(Volume < input$cutoff)}else{tableR}, Animal+Side+Group~., 
+                       value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+        endtime["Dead"]<-dcast(tableR, Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") >= input$cutoff
         table_tumor<<-endtime
         
         g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor),
@@ -543,19 +543,19 @@ server <- function(input, output) {
   output$stats<-renderPrint({
     stattest<-"dunn"
     oneside<-""
-    if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
-      observeEvent(analysis$taula_def, {})
-      table<-analysis$taula_def
+    if (!is.null(input$file_analy) & !is.null(analysis$taula)){
+      observeEvent(analysis$taula, {})
+      table<-analysis$taula
       if (input$vacc == "No"){
         table<-filter(table, !is.na(Volume))
-        summary(aov(Volume~Group+Timepoint+Error(`ID animal`+`ID tumor`), data=table))
+        summary(aov(Volume~Group+DayPostInoc+Error(Animal+Side), data=table))
       }else{
         for (side in c("L","R")){
-          tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
-          if (length(unique(tableR$Volume)) > 1 & length(unique(tableR$Timepoint)) > 1){
+          tableR<-filter(table, Side == side) %>% filter(!is.na(Volume))
+          if (length(unique(tableR$Volume)) > 1 & length(unique(tableR$DayPostInoc)) > 1){
             print(paste0("Side: ",side))
-            # print(summary(aov(Volume~Group+Timepoint+Error(paste0(ID animal,Cage)), data=tableR)))
-            print(summary(aov(Volume~Group+Timepoint+Error(`ID animal`), data=tableR)))
+            # print(summary(aov(Volume~Group+DayPostInoc+Error(paste0(Animal,Cage)), data=tableR)))
+            print(summary(aov(Volume~Group+DayPostInoc+Error(Animal), data=tableR)))
           }
         }
       }