Implementar la posibilidad de eliminar los ratones que hayan muerto prematuramente.

invivos/app.R

@@ -48,6 +48,7 @@ ui <- fluidPage(
                          checkboxInput("filter_stats","Filtrar Estadística"),
                          checkboxInput("increase_volume","Usar Incremento de Volumen"),
                          checkboxInput("operated","Cortar al operar", value = TRUE),
+                         checkboxInput("dead","Eliminar ratones muertos", value = FALSE),
                          downloadButton("downloadVolume", "Descargar Volúmenes")
                        ),
                        mainPanel(
@@ -456,11 +457,17 @@ server <- function(input, output) {
         firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% 
           select(DayPostInoc, Side) %>% unique() %>% 
           group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
-        
+        deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+          pull(Animal)
+        print(deadmice)
         if (input$operated == TRUE){
           for (i in 1:nrow(firstoper)){
             table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
           } 
+        }else{
+          if(input$dead == TRUE){
+            table<-table %>% filter(!Animal %in% deadmice)
+          }
         }
         
         ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
@@ -480,6 +487,12 @@ server <- function(input, output) {
         
         if (input$operated == TRUE){
           table<-table %>% filter(DayPostInoc < firstoper)
+        }else{
+          deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+            pull(Animal)
+          if(input$dead == TRUE){
+            table<-table %>% filter(!Animal %in% deadmice)
+          }
         }
 
         ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
@@ -518,6 +531,20 @@ server <- function(input, output) {
       table<-rbind(table, basal)
       
       if (input$vacc == "Sí"){
+        firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% 
+          select(DayPostInoc, Side) %>% unique() %>% 
+          group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
+        if (input$operated == TRUE){
+          for (i in 1:nrow(firstoper)){
+            table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
+          } 
+        }else{
+          if(input$dead == TRUE){
+            deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+              pull(Animal)
+            table<-table %>% filter(!Animal %in% deadmice)
+          }
+        }
         ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Animal))+
           # geom_errorbar(stat="summary", width=0.05)+
           geom_line()+
@@ -528,6 +555,19 @@ server <- function(input, output) {
           labs(x="Days after tumor inoculation")+
           theme_bw()  
       }else{
+        firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% 
+          pull(DayPostInoc) %>% min(na.rm = T)
+        print(firstoper)
+        
+        if (input$operated == TRUE){
+          table<-table %>% filter(DayPostInoc < firstoper)
+        }else{
+          deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+            pull(Animal)
+          if(input$dead == TRUE){
+            table<-table %>% filter(!Animal %in% deadmice)
+          }
+        }
         ggplot(table, aes(DayPostInoc, Volume, color=Group, group=paste0(Animal, Side)))+
           # geom_errorbar(stat="summary", width=0.05)+
           geom_line()+
@@ -713,6 +753,12 @@ server <- function(input, output) {
               for (i in 1:nrow(firstoper)){
                 table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
               } 
+            }else{
+              if(input$dead == TRUE){
+                deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+                  pull(Animal)
+                table<-table %>% filter(!Animal %in% deadmice)
+              }
             }
             std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
             errbar<-table %>% group_by(Group,Side,DayPostInoc) %>% 
@@ -739,7 +785,14 @@ server <- function(input, output) {
             
             if (input$operated == TRUE){
               table<-table %>% filter(DayPostInoc < firstoper)
+            }else{
+              deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+                pull(Animal)
+              if(input$dead == TRUE){
+                table<-table %>% filter(!Animal %in% deadmice)
+              }
             }
+            
             std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
             errbar<-table %>% group_by(Group, DayPostInoc) %>% 
               summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% 
@@ -761,6 +814,22 @@ server <- function(input, output) {
         }
         if (input$fig_id == "Cinética Individual"){
           if (input$vacc == "Sí"){
+            firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% 
+              select(DayPostInoc, Side) %>% unique() %>% 
+              group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
+            
+            if (input$operated == TRUE){
+              for (i in 1:nrow(firstoper)){
+                table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
+              } 
+            }else{
+              if(input$dead == TRUE){
+                deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+                  pull(Animal)
+                table<-table %>% filter(!Animal %in% deadmice)
+              }
+            }
+            
             g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
               scale_x_continuous(expand = expansion(mult = c(0,0.0)),
                                  breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),
@@ -768,6 +837,20 @@ server <- function(input, output) {
               facet_grid(factor(Side, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
               theme_bw()
           }else{
+            firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% 
+              pull(DayPostInoc) %>% min(na.rm = T)
+            print(firstoper)
+            
+            if (input$operated == TRUE){
+              table<-table %>% filter(DayPostInoc < firstoper)
+            }else{
+              deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% 
+                pull(Animal)
+              if(input$dead == TRUE){
+                table<-table %>% filter(!Animal %in% deadmice)
+              }
+            }
+            
             g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
               scale_x_continuous(expand = expansion(mult = c(0,0.0)),
                                  breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),