Corretgir error.

invivos/app.R

@@ -42,6 +42,7 @@ ui <- fluidPage(
                          selectInput(inputId = "vacc", "Experimento de Vacunación", selected = "No", choices = c("Sí","No")),
                          uiOutput('cutoffUI'),
                          checkboxInput("filter_stats","Filtrar Estadística"),
+                         checkboxInput("increase_volume","Usar Incremento de Volumen"),
                          downloadButton("downloadVolume", "Descargar Volúmenes")
                        ),
                        mainPanel(
@@ -63,7 +64,10 @@ ui <- fluidPage(
                                     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),
+                                    textInput("xaxis", label="Etiqueta Eje X", value=""),
+                                    textInput("yaxis", label="Etiqueta Eje Y", value=""),
+                                    sliderInput("errorbar-width", "% Ancho errorbars", min=0.0, max=1, step=0.05, value=0.05),
+                                    sliderInput("line-size", "Tamaño línea", min=0.1, max=3, step=0.1, value=0.5),
                                     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 = "logscale", label="Escala logarítmica eje Y", value=F),
@@ -100,8 +104,12 @@ server <- function(input, output) {
         taula$Minor<-taula$Minor
         taula["Volume"]<-((taula$Major*taula$Minor*taula$Minor)*(pi/6))
       }
+      if ("TS" %in% colnames(taula)){
+        taula<-dcast(taula, Cage+`ID animal`+`ID tumor`+Group~TS, value.var = "0")
+        taula["Volume"]<-taula$`TS-Deep`*taula$`TS-Length`*taula$`TS-Width`*pi/6
+      }
       dades$taula<-taula
-      dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2, colName=F)[,1]
+      dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2, colNames=F)[,1]
       if (readxl::excel_sheets(input$file_sizes$datapath) %>% length > 2){
         dades$sex<-read.xlsx(input$file_sizes$datapath, sheet = 3, sep.names = " ")
       }
@@ -122,7 +130,7 @@ server <- function(input, output) {
   output$lowcut<-renderUI({
     if (!is.null(dades$taula)){
       cut.max<-round(max(dades$taula$Volume, na.rm = T), 2)
-      step<-round(max(dades$taula$Volume, na.rm = T)/20, 2)
+      step<-round(max(dades$taula$Volume, na.rm = T)/100, 2)
       sliderInput("lowcut", "Corte inferior", min=0, max=cut.max, step=step, value=0)
     }
   })
@@ -195,7 +203,7 @@ server <- function(input, output) {
           test.list[data]<-summary(res.aov)[[1]][[4]][1]
         }
       }
-      index<-which(unlist(lvn.list) == min(unlist(lvn.list)[which(unlist(pval.list) %in% sort(unlist(pval.list), decreasing = T)[1:20])]))
+      index<-which(unlist(lvn.list) == min(unlist(lvn.list)[which(unlist(pval.list) %in% sort(unlist(pval.list), decreasing = T)[1:20])]))[1]
       # print(df_sex)
       df_def[[sex.var]]<-merge(df_sex %>% select(-group), ind.list[[index]])
     }
@@ -207,8 +215,10 @@ server <- function(input, output) {
     }
     df_def<-merge(
       if(!is.null(dades$sex)){merge(dades$taula, dades$sex)}else{dades$taula %>% add_column(sex="undefined")} %>% select(-Group), 
-      df_def[,c("ID animal", "group")] %>% unique, all=T, by="ID animal") %>% 
-      select(c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, Major, Minor, group))
+      df_def[,c("ID animal", "group")] %>% unique, all=T, by="ID animal")
+    if("DPV" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, Major, Minor, group))}
+    if("TS-Deep" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, `TS-Deep`,`TS-Length`,`TS-Width`, group))}
+    
     df_def[!paste0(df_def$`ID animal`, df_def$`ID tumor`) %in% paste0(df$`ID animal`, df$`ID tumor`),"group"]<-NA
     dades$db<-df_def
 
@@ -379,6 +389,15 @@ 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$Timepoint)))))
+      if (input$increase_volume){
+        timepoints<-unique(table$Timepoint)
+        table<-table %>% select(-Major, -Minor) %>% 
+          spread(Timepoint, Volume) %>% 
+          mutate(across(all_of(timepoints), function(x){(x*100/`0`)-100})) %>%
+          gather(Timepoint, Volume, -Cage, -`ID animal`, -`ID tumor`, -Group) %>% 
+          mutate(Volume=case_when(Volume < 0 ~ 0, T~Volume))
+      }
+      table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint)))))
       analysis$taula_def<-table
       analysis$taula_vol<-dcast(table, Cage+`ID animal`+`ID tumor`~Timepoint,value.var = "Volume")
       table_plot<-dcast(dcast(table %>% filter(!is.na(Volume)), `ID animal`+Group+Timepoint~., value.var = "Volume", fun.aggregate = mean), Group~Timepoint)
@@ -389,6 +408,7 @@ server <- function(input, output) {
     if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
       observeEvent(analysis$taula_def, {})
       table<-analysis$taula_def
+      
       if (input$vacc == "Sí"){
         ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
           geom_errorbar(stat="summary", width=0.05)+
@@ -585,30 +605,60 @@ server <- function(input, output) {
       if (input$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) %>% 
+              summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% 
+              mutate(Timepoint2=as.numeric(as.character(Timepoint))) %>% 
+              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(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
+                                 breaks=sort(unique(errbar$Timepoint2)),
+                                 limits = c(0,max(as.numeric(as.character(table$Timepoint)))*1.1))+
               facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~., scale="free_y")+
-              theme_bw()  
+              theme_bw()+
+              geom_segment(data=errbar, aes(y=mean, yend=mean+std, x=Timepoint2,  xend=Timepoint2))+
+              geom_segment(data=errbar, aes(y=mean+std, yend=mean+std,
+                                            x=x,xend=xend))
           }else{
-            g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=Group))+
-              theme_bw()
+            std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
+            errbar<-table %>% group_by(Group, Timepoint) %>% 
+              summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% 
+              mutate(Timepoint2=as.numeric(as.character(Timepoint))) %>% 
+              mutate(x=Timepoint2-input$`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))+
+              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))
           }
         }
         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(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
+                                 breaks=sort(unique(as.numeric(as.character(table$Timepoint)))),
+                                 limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
               facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
               theme_bw()  
           }else{
-            g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=`ID animal`))+
+            g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=`ID animal`))+
+              scale_x_continuous(expand = expansion(mult = c(0,0.0)), 
+                                 breaks=sort(unique(as.numeric(as.character(table$Timepoint)))),
+                                 limits = c(0,max(as.numeric(as.character(table$Timepoint)))*1.1))+
               facet_wrap(.~Group)+
               theme_bw()
           }
         }
         
-        g<-g+geom_errorbar(stat="summary", width=input$`errorbar-width`)+
-          geom_line(stat="summary")+
+        g<-g+
+          # geom_errorbar(stat="summary", width=input$`errorbar-width`)+
+          geom_line(stat="summary", size=input$`line-size`)+
           geom_point(stat="summary", size=input$`point-size`)+
           labs(x="Days after tumor challenge")+
           scale_y_continuous(expand = expansion(mult = c(0,0.05)))
@@ -616,6 +666,12 @@ server <- function(input, output) {
         if (input$theme == "BW"){
           g<-g+theme_bw(base_size = input$`font-size`)
         }
+        if (input$xaxis != ""){
+          g<-g+xlab(input$xaxis)
+        }
+        if (input$yaxis != ""){
+          g<-g+ylab(input$yaxis)
+        }
         if (input$theme == "Classic"){
           g<-g+theme_classic(base_size = input$`font-size`)  
         }