He añadido una pestaña para exportar imágenes. También he añadido el timepoint 0 cuando no existe para que los gráficos empiezen siempre en él.

invivos/app.R

@@ -45,7 +45,26 @@ ui <- fluidPage(
                          h3('Estadística'),
                          verbatimTextOutput('stats'),
                          tableOutput('tab_stats')
-                       ))
+                       )),
+              tabPanel("Exportar",
+                       sidebarPanel(width=2,
+                                    h3('Seleccionar figura'),
+                                    selectInput("fig_id", "", selected="", choices=c("Cinética Grupo", "Cinética Individual", "Survival")),
+                                    h3('Formato'),
+                                    sliderInput("width", "Ancho", min=1000, max=20000, step=1000, value=10000),
+                                    sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000),
+                                    textInput("colors", label="Colors", value=""),
+                                    sliderInput("errorbar-width", "% Ancho errorbars", min=0.05, max=1, step=0.05, value=0.05),
+                                    sliderInput("point-size", "Tamaño puntos", min=1, max=10, step=1, value=3),
+                                    sliderInput("font-size", "Tamaño textos", min=5, max=30, step=1, value=11),
+                                    checkboxInput(inputId = "legend", label = "Mostrar llegenda", value = T),
+                                    selectInput("theme", "Seleccionar Tema", selected="BW", choices=c("BW", "Default", "Classic")),
+                                    downloadButton("downloadPicture", "Exportar")
+                       ),
+                       mainPanel(
+                         uiOutput("expPlotUI")
+                       )
+              )
               )
    
    )
@@ -229,9 +248,12 @@ server <- function(input, output) {
       if ("ID.tumor" %in% colnames(table)){table<-rename(table, "ID tumor"=`ID.tumor`)}
       # table[table$ID.tumor == "R","0"]<-NA
       col_nodays<-c("ID", "Cage","Group", "ID.animal","ID animal", "ID.tumor", "ID tumor", "TS","DPV", "Absorbance")
+      print(grep(0, colnames(table)[!colnames(table) %in% col_nodays]))
+      if (length(grep(0, colnames(table)[!colnames(table) %in% col_nodays])) == 0){
+        table["0"]<-0
+      }
       table<-melt(table, id=colnames(table)[colnames(table) %in% col_nodays], variable.name = "Timepoint")
       table$Timepoint<-gsub("[A-Za-z ]","",table$Timepoint)
-      table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint)))))
       if ("DPV" %in% colnames(table)){
         table<-dcast(table, Cage+`ID animal`+`ID tumor`+Group+Timepoint~DPV, value.var = "value")
         table$Major<-table$Major/1000
@@ -244,6 +266,7 @@ server <- function(input, output) {
       }
       if (!"Volume" %in% colnames(table)){table<-rename(table, "Volume"=value)}
       table<-table %>% filter(!is.na(Group))
+      table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint)))))
       analysis$taula_def<-table
       table_plot<-dcast(dcast(table %>% filter(!is.na(Volume)), `ID animal`+Group+Timepoint~., value.var = "Volume", fun.aggregate = mean), Group~Timepoint)
       table_plot
@@ -373,6 +396,88 @@ server <- function(input, output) {
       }
     }
   })
+  
+  output$expPlotUI<- renderUI({
+    observeEvent(analysis$taula_def, {})
+    if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
+      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$taula_def
+      
+      print(head(table))
+      
+      if (input$fig_id == "Cinética Grupo"){
+        if (input$vacc == "Sí"){
+          g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
+            scale_x_continuous(expand = expansion(mult = c(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
+            facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~., scale="free_y")+
+            theme_bw()  
+        }else{
+          g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=Group))+
+            theme_bw()
+        }
+      }
+      if (input$fig_id == "Cinética Individual"){
+        if (input$vacc == "Sí"){
+          g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
+            scale_x_continuous(expand = expansion(mult = c(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
+            facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
+            theme_bw()  
+        }else{
+          g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=`ID animal`))+
+            facet_wrap(.~Group)+
+            theme_bw()
+        }
+      }
+      
+      g<-g+geom_errorbar(stat="summary", width=input$`errorbar-width`)+
+        geom_line(stat="summary")+
+        geom_point(stat="summary", size=input$`point-size`)+
+        labs(x="Days after tumor challenge")+
+        scale_y_continuous(expand = expansion(mult = c(0,0.05)))
+      
+      if (input$theme == "BW"){
+        g<-g+theme_bw(base_size = input$`font-size`)
+      }
+      if (input$theme == "Classic"){
+        g<-g+theme_classic(base_size = input$`font-size`)  
+      }
+      if (input$theme == "Default"){
+        g<-g+theme_gray(base_size = input$`font-size`)
+      }
+      # g<-g+theme(axis.text.x=element_text(angle=45, hjust=1))
+      if (input$legend == F){
+        g<-g+guides(color=FALSE, fill=FALSE)
+      }
+      if (input$colors != ""){
+        v_col<-strsplit(input$colors, ",")[[1]]
+        g<-g+scale_color_manual(values=v_col)+
+          scale_fill_manual(values=v_col)
+      }
+      dades$plot<<-g
+      g
+    }
+  }, res=72)
+  
+  output$downloadPicture <- downloadHandler(
+    filename = function() {
+      paste("Figura", ".png", sep="")
+    },
+    content = function(file){
+      print(file)
+      # tempReport <- file.path(tempdir(), "elispots.Rmd")
+      # file.copy("elispots.Rmd", tempReport, overwrite = TRUE)
+      png(file, width = input$width, height=input$height, units = "px", res=720)
+      plot(dades$plot)
+      dev.off()
+      
+    })
+  
 }
 
 # Run the application