From c5229e858afa9f9ce06d6ad6f75f0c1c0d129911 Mon Sep 17 00:00:00 2001
From: marcelcosta <marcelcosta@mcosta.cat>
Date: Wed, 14 Sep 2022 12:16:01 +0200
Subject: [PATCH] =?UTF-8?q?Cambios=20en=20los=20gr=C3=A1ficos=20de=20l?=
 =?UTF-8?q?=C3=ADneas=20en=20la=20exportaci=C3=B3n.?=
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---
 invivos/app.R | 34 +++++++++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/invivos/app.R b/invivos/app.R
index 63eea6e..315aabc 100755
--- a/invivos/app.R
+++ b/invivos/app.R
@@ -63,7 +63,8 @@ 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),
+                                    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),
@@ -590,25 +591,44 @@ server <- function(input, output) {
               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()
+            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(errbar$Timepoint2)),
+                                 limits = c(0, (round(max(as.numeric(as.character(table$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)))