From 882e7eab470d4c45ef33224ad363ee0bda812948 Mon Sep 17 00:00:00 2001
From: Costa <47926492N@ICO.SCS.local>
Date: Thu, 24 Feb 2022 14:45:24 +0100
Subject: [PATCH] =?UTF-8?q?Detectar=20si=20hay=20pesta=C3=B1a=20para=20sex?=
 =?UTF-8?q?o=20de=20los=20ratones=20y=20adaptarse.?=
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---
 invivos/app.R | 64 +++++++++++++++++++++++++++++++++------------------
 1 file changed, 41 insertions(+), 23 deletions(-)

diff --git a/invivos/app.R b/invivos/app.R
index aae2bce..1f9436c 100755
--- a/invivos/app.R
+++ b/invivos/app.R
@@ -1,8 +1,6 @@
 library(shiny)
-# library(ggplot2)
 library(reshape2)
 library(openxlsx)
-# library(dplyr)
 library(car)
 library(ggbeeswarm)
 library(gtools)
@@ -104,7 +102,9 @@ server <- function(input, output) {
       }
       dades$taula<-taula
       dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2, colName=F)[,1]
-      dades$sex<-read.xlsx(input$file_sizes$datapath, sheet = 3, sep.names = " ")
+      if (readxl::excel_sheets(input$file_sizes$datapath) %>% length > 2){
+        dades$sex<-read.xlsx(input$file_sizes$datapath, sheet = 3, sep.names = " ")
+      }
     }
   })
   output$firstPlot <- renderPlot({
@@ -150,7 +150,12 @@ server <- function(input, output) {
     low_cuttof<-input$lowcut
     # print(up_cuttof)
     df<-df[df$Volume < up_cuttof & df$Volume >= low_cuttof,]
-    df<-merge(df, dades$sex)
+    if (is.null(dades$sex)){
+      df<-add_column(df, sex="undefined")
+    }else{
+      df<-merge(df, dades$sex)
+    }
+    
     
     # df["Mouse"]<-gsub("[a-zA-Z]", "", df$MouseID)
     # print(df$Volume)
@@ -159,7 +164,7 @@ server <- function(input, output) {
     ngroup<-length(dades$groups)
     df_def<-list()
     # print(head(df))
-    for (sex.var in c("male","female")){
+    for (sex.var in unique(df$sex)){
       # print(sex.var)
       df_sex<-df %>% filter(`sex` == sex.var)
       ind.list<-list()
@@ -194,33 +199,46 @@ server <- function(input, output) {
       # print(df_sex)
       df_def[[sex.var]]<-merge(df_sex %>% select(-group), ind.list[[index]])
     }
-    # df_def<-do.call(rbind, c(df_def, make.row.names=F))
+    df_def<-do.call(rbind, c(df_def, make.row.names=F))
     # lapply(df_def, function(x) x %>% as_tibble %>% print(n=Inf))
-    df_def<-rbind(df_def[[1]], df_def[[2]], make.row.names=F)
+    # df_def<-rbind(df_def[[1]], df_def[[2]], make.row.names=F)
     if ("Group" %in% colnames(df_def)){
       df_def<-df_def %>% select(-"Group") 
     }
-    df_def<-merge(merge(dades$taula, dades$sex) %>% 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<-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[!paste0(df_def$`ID animal`, df_def$`ID tumor`) %in% paste0(df$`ID animal`, df$`ID tumor`),"group"]<-NA
     dades$db<-df_def
 
-    ggarrange(
-    ggplot(df_def, aes(group, Volume))+
-      geom_boxplot(outlier.alpha = F)+
-      geom_jitter(width=0.25, aes(color=sex))+
-      geom_point(stat="summary", color="blue", size=3)+
-      theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)),
-      # lims(y=c(0,max(df_def$Volume)+10))
-    ggarrange(
-      ggplot(df_def, aes(sex, Volume))+
+    if (is.null(dades$sex)){
+      ggplot(df_def, aes(group, Volume))+
         geom_boxplot(outlier.alpha = F)+
-        geom_quasirandom(width=0.3),
-      ggplot(df_def, aes(group, fill=sex))+
-        geom_bar(stat="count", color="black", position="dodge")+
-        guides(fill="none")+
-        theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)), ncol = 1, heights = c(0.35, 0.65)),
-    nrow = 1, aligh="h", widths = c(0.65, 0.35))
+        geom_jitter(width=0.25)+
+        geom_point(stat="summary", color="blue", size=3)+
+        theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5))
+    }else{
+      ggarrange(
+        ggplot(df_def, aes(group, Volume))+
+          geom_boxplot(outlier.alpha = F)+
+          geom_jitter(width=0.25, aes(color=sex))+
+          geom_point(stat="summary", color="blue", size=3)+
+          theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)),
+        # lims(y=c(0,max(df_def$Volume)+10))
+        ggarrange(
+          ggplot(df_def, aes(sex, Volume))+
+            geom_boxplot(outlier.alpha = F)+
+            geom_quasirandom(width=0.3),
+          ggplot(df_def, aes(group, fill=sex))+
+            geom_bar(stat="count", color="black", position="dodge")+
+            guides(fill="none")+
+            theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)), ncol = 1, heights = c(0.35, 0.65)),
+        nrow = 1, aligh="h", widths = c(0.65, 0.35))
+    }
+
   })
+  
   output$distPlot <- renderPlot({
     observeEvent(dades$taula, {})
     if (!is.null(dades$taula)){