Cambiar sistema de estadística a rstatix y ggpubr

README.md

@@ -0,0 +1,7 @@
+# Analizador de ELISPOTs
+
+En proceso/pendiente:
+
++ Estadística de paquetes ggpubr y rstatix.
++ Mejorar editor.
+    + ggedit podría servir pero no parece que la estadística de ggpubr sea compatible.

app.R

@@ -1,13 +1,16 @@
 library(shiny)
 library(openxlsx)
 library(readxl)
-library(ggplot2)
+# library(ggplot2)
 library(reshape2)
-library(dplyr)
+# library(dplyr)
 library(ggbeeswarm)
 library(magrittr)
 library(flextable)
 source("funcions.R")
+library(tidyverse)
+library(rstatix)
+library(ggpubr)
 
 ui <- fluidPage(
   #Navbar
@@ -119,17 +122,13 @@ server <- function(input, output) {
                 dades$maps<<-t_maps
             }else{
               if (input$test == "T-test (adj Holm)"){
-                t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest")
+                t_stats<-t %>% rename("Condition"="variable") %>% group_by(Condition) %>% t_test(value~Groups)
               }
               if (input$test == "Wilcoxon (adj Holm)"){
-                t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "wilcox")
+                t_stats<-t %>% rename("Condition"="variable") %>% group_by(Condition) %>% wilcox_test(value~Groups)
               }
               
               dades$stats<<-t_stats
-              t_stats<-t_stats %>% filter(p.signif != "ns")
-              
-              t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups")
-              dades$maps<<-t_maps
             }
             if (length(unique(dades$taula %>% pull(Groups))) < 2){
               dades$stats<<-null
@@ -145,7 +144,7 @@ server <- function(input, output) {
                   need(exists("mock_mean"), "No se puede elegir positividad con múltiples mocks")
                 )
                 if (exists("mock_mean")){
-                  ggplot(melt(t_substr, id=ids), aes(variable, value))+
+                  g<-ggplot(melt(t_substr, id=ids), aes(variable, value))+
                     labs(x="", y="Spots/2.5*10^5 cells")+
                     # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
                     geom_hline(data=mock_mean, aes(color=Groups, yintercept = `.`))+
@@ -162,7 +161,7 @@ server <- function(input, output) {
                 
             }else{
                 ids=c("Mice", "Groups", c(ctrl, mock)[c(ctrl, mock) %in% colnames(t_substr)])
-                ggplot(melt(t_substr, id=ids), aes(variable, value))+
+                g<-ggplot(melt(t_substr, id=ids, variable.name = "Condition"), aes(Condition, value))+
                     labs(x="", y="Spots/2.5*10^5 cells")+
                     # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
                     # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
@@ -170,11 +169,17 @@ server <- function(input, output) {
                     geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+
                     # geom_quasirandom(width=0.2, position=position_dodge(), shape=21)+
                     scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
-                    geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
+                    # geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
-                    geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
+                    # geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
                     theme_bw()+
                     theme(axis.text.x=element_text(angle=45, hjust=1))
             }
+            if (input$showstats == T){
+              stat.pos<-t_stats %>% add_xy_position(x="Condition", step.increase = 0.06, dodge = 0.75)
+              g+stat_pvalue_manual(stat.pos,hide.ns = T)
+            }else{
+              g
+            }
         }
         
     })
@@ -204,12 +209,11 @@ server <- function(input, output) {
       if (!is.null(dades$final)){
         print(dades$stats)
         t_substr<-dades$final
-        t_stats<-dades$stats %>% filter(p.signif != "ns")
+        t_stats<-dades$stats
-        t_maps<-dades$maps
 
         ids<-c("Mice", "Groups")
         set.seed(123)
-        g<-ggplot(melt(t_substr, id=ids), aes(variable, value))+
+        g<-ggplot(melt(t_substr, id=ids, variable.name="Condition"), aes(Condition, value))+
           labs(x="", y="Spots/2.5*10^5 cells")+
           geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0, position=position_dodge(width=0.8),width=input$`boxplot-width`)+
           geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=input$`point-size`)+
@@ -224,13 +228,13 @@ server <- function(input, output) {
           g<-g+theme_gray(base_size = input$`font-size`)
         }
         g<-g+theme(axis.text.x=element_text(angle=45, hjust=1))
-        if (input$stats2 == T){
-          g<-g+geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
-            geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")
-        }
         if (input$legend == F){
           g<-g+guides(color=FALSE, fill=FALSE)
         }
+        if (input$stats2 == T){
+          stat.pos<-dades$stats %>% add_xy_position(x="Condition", step.increase = 0.06, dodge = 0.75)
+          g<-g+stat_pvalue_manual(stat.pos,hide.ns = T)
+        }
         if (input$colors != ""){
           v_col<-strsplit(input$colors, ",")[[1]]
           g<-g+scale_color_manual(values=v_col)+