From fd6493320fa7ccd735c87a000f68e20d27708c4f Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Thu, 16 Feb 2023 14:42:02 +0100
Subject: [PATCH] =?UTF-8?q?Correcci=C3=B3=20de=20bugs=20a=20l'exportar=20s?=
 =?UTF-8?q?urvival.?=
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---
 invivos/app.R | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/invivos/app.R b/invivos/app.R
index 38b7f7a..8bab990 100755
--- a/invivos/app.R
+++ b/invivos/app.R
@@ -397,7 +397,7 @@ server <- function(input, output) {
         print(levels)
         table$Group<-factor(table$Group, levels=levels)
         table<-filter(table, !is.na(Group))
-      }
+      }else(table$Group<-factor(table$Group))
       print(str(table))
       analysis$taula<-table
     }
@@ -816,23 +816,24 @@ server <- function(input, output) {
           hues <- seq(15, 375, length=n+1)
           hcl(h=hues, l=l, c=100)[1:n]
         }
+
         if (input$vacc == "Sí"){
           g<-list()
           count<-1
           for (side in c("L","R")){
             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
+            endtime<-dcast(tableR %>% filter(Volume < (input$cutoff*as.numeric(input$unit_fact))), 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$cutoff*as.numeric(input$unit_fact))
             table_tumor<-endtime
             if (input$colors != ""){
-              col<-input$colors
+              col<-strsplit(input$colors, ",")[[1]]
             }else{
               col<-gg_color_hue(length(unique(endtime$Group)))
             }
-            g[[count]]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor),
+            table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group))
+            g[[count]]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor),
                                 pval = T, pval.method = T,
                                 title = side,
-                                # legend.labs = paste(c("< median", ">= median"), "MICA"),
                                 ggtheme=theme_classic(base_size=input$`font-size`),
                                 palette = col
             )
@@ -842,18 +843,18 @@ server <- function(input, output) {
           
         }else{
           tableR<-table %>% filter(!is.na(Volume))
-          endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Animal+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
-          endtime["Dead"]<-dcast(tableR, Animal+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
+          endtime<-dcast(tableR %>% filter(Volume < (input$cutoff*as.numeric(input$unit_fact))), Animal+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
+          endtime["Dead"]<-dcast(tableR, Animal+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > (input$cutoff*as.numeric(input$unit_fact))
           table_tumor<-endtime
           if (input$colors != ""){
-            col<-input$colors
+            col<-strsplit(input$colors, ",")[[1]]
           }else{
             col<-gg_color_hue(length(unique(table_tumor$Group)))
           }
-          g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor),
+          table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group))
+          g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor),
                         pval = T, pval.method = T,
-                        # legend.labs = paste(c("< median", ">= median"), "MICA"),
-                        ggtheme=theme_classic(base_size=input$`font-size`),
+                        # ggtheme=theme_classic(base_size=input$`font-size`),
                         palette = col
           )
         }