Cambio de formato de la pestaña exportar.

invivos/app.R

@@ -621,48 +621,69 @@ server <- function(input, output) {
   
   ##Exportar
   output$expPlotUI<- renderUI({
-    observeEvent(analysis$taula_def, {})
-    if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
+    observeEvent(analysis$taula, {})
+    if (!is.null(input$file_analy) & !is.null(analysis$taula)){
       plotOutput("expPlot", width=paste0(input$width/10,"px"), height = paste0(input$height/10, "px"))
     }
   })
   
   output$expPlot <- renderPlot({
-    observeEvent(analysis$taula_def, {})
-    if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
-      table<-analysis$taula_def
-      
+    observeEvent(analysis$taula, {})
+    if (!is.null(input$file_analy) & !is.null(analysis$taula)){
+      table<-analysis$taula
+      animals<-unique(table$Animal)
+      sides<-unique(table$Side)
+      groups<-table %>% select(Animal, Group) %>% unique() %>% pull(Group)
+      basal<-data.frame(
+        Cage="",
+        Animal=rep(animals, each=length(sides)),
+        Date="",
+        DayPostInoc=0,
+        Group=rep(groups, each=length(sides)),
+        Side=rep(sides, length(animals)),
+        Weight="",
+        Long="",
+        Wide="",
+        Volume=0,
+        Observations=""
+      )
+      table<-rbind(table, basal)
       if (input$fig_id %in% c("Cinética Grupo", "Cinética Individual")){
         if (input$fig_id == "Cinética Grupo"){
           if (input$vacc == "Sí"){
             std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
-            errbar<-table %>% group_by(Group,`ID tumor`, Timepoint) %>% 
+            errbar<-table %>% group_by(Group,Side,DayPostInoc) %>% 
               summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% 
-              mutate(Timepoint2=as.numeric(as.character(Timepoint))) %>% 
+              mutate(Timepoint2=as.numeric(as.character(DayPostInoc))) %>% 
               mutate(x=Timepoint2-input$`errorbar-width`, xend=Timepoint2+input$`errorbar-width`)
             
-            g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
-              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
-                                 breaks=sort(unique(errbar$Timepoint2)),
-                                 limits = c(0,max(as.numeric(as.character(table$Timepoint)))*1.1))+
-              facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~., scale="free_y")+
+            g<-ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
+              geom_errorbar(stat="summary", width=0.05)+
+              geom_line(stat="summary")+
+              geom_point(stat="summary")+
+              facet_grid(factor(Side, labels = c("Vaccination", "Rechallenge"))~., scale="free_y")+
+              labs(x="Days after tumor inoculation")+
+              scale_y_continuous(expand = expansion(mult = c(0,0.05)))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.05)), limits = c(0, (round(max(table$DayPostInoc) / 5)+1)*5))+
               theme_bw()+
               geom_segment(data=errbar, aes(y=mean, yend=mean+std, x=Timepoint2,  xend=Timepoint2))+
               geom_segment(data=errbar, aes(y=mean+std, yend=mean+std,
                                             x=x,xend=xend))
           }else{
             std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
-            errbar<-table %>% group_by(Group, Timepoint) %>% 
+            errbar<-table %>% group_by(Group, DayPostInoc) %>% 
               summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% 
-              mutate(Timepoint2=as.numeric(as.character(Timepoint))) %>% 
+              mutate(Timepoint2=as.numeric(as.character(DayPostInoc))) %>% 
               mutate(x=Timepoint2-input$`errorbar-width`, xend=Timepoint2+input$`errorbar-width`)
             
-            g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
-              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
-                                 breaks=sort(unique(errbar$Timepoint2)),
-                                 limits = c(0,max(as.numeric(as.character(table$Timepoint)))*1.1))+
-              # limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
+            g<-ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
+              geom_errorbar(stat="summary",width=0.05)+
+              geom_line(stat="summary")+
+              geom_point(stat="summary")+
+              labs(x="Days after tumor challenge")+
+              scale_y_continuous(expand = expansion(mult = c(0,0.05)))+
               theme_bw()+
+              theme(axis.text.x=element_text(angle=45, hjust=1))+
               geom_segment(data=errbar, aes(y=mean, yend=mean+std, x=Timepoint2,  xend=Timepoint2))+
               geom_segment(data=errbar, aes(y=mean+std, yend=mean+std,
                                             x=x,xend=xend))
@@ -670,17 +691,17 @@ server <- function(input, output) {
         }
         if (input$fig_id == "Cinética Individual"){
           if (input$vacc == "Sí"){
-            g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=`ID animal`))+
-              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
-                                 breaks=sort(unique(as.numeric(as.character(table$Timepoint)))),
-                                 limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
-              facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
-              theme_bw()  
+            g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.0)),
+                                 breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),
+                                 limits = c(0, (round(max(as.numeric(as.character(table$DayPostInoc))) / 5)+1)*5))+
+              facet_grid(factor(Side, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
+              theme_bw()
           }else{
-            g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=`ID animal`))+
-              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
-                                 breaks=sort(unique(as.numeric(as.character(table$Timepoint)))),
-                                 limits = c(0,max(as.numeric(as.character(table$Timepoint)))*1.1))+
+            g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.0)),
+                                 breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),
+                                 limits = c(0,max(as.numeric(as.character(table$DayPostInoc)))*1.1))+
               facet_wrap(.~Group)+
               theme_bw()
           }
@@ -729,9 +750,9 @@ server <- function(input, output) {
           g<-list()
           count<-1
           for (side in c("L","R")){
-            tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
-            endtime<-dcast(tableR %>% filter(Volume < input$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$cutoff
             table_tumor<-endtime
             if (input$colors != ""){
               col<-input$colors
@@ -751,8 +772,8 @@ server <- function(input, output) {
           
         }else{
           tableR<-table %>% filter(!is.na(Volume))
-          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
+          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
           table_tumor<-endtime
           if (input$colors != ""){
             col<-input$colors