correction

app.R

@@ -78,7 +78,7 @@ server <- function(input, output) {
               t_substr<-merge(t_substr, unique(dades$taula[c("Mice","Groups")]), id="Mice")
               t_substr$Groups<-as.factor(t_substr$Groups)
             }            
-            
+
             t_substr_gp<-t_substr
             t_substr_gp[3:ncol(t_substr)]<-apply(t_substr[3:ncol(t_substr)], 2, function(x) gsub(".",",",x, fixed=T))
             t_substr_gp<-t_substr_gp[order(factor(t_substr_gp$Mice, levels = unique(table$Mice))),]
@@ -87,7 +87,7 @@ server <- function(input, output) {
             write.xlsx(doc, "data4graphpad.xlsx",rowNames=T)
             
             t<-melt(t_substr[,!colnames(t_substr) %in% c(ctrl, mock)])
-            
+
             if (input$showstats == F){
                 t_stats<-as.data.frame(matrix(nrow=0, ncol=6))
                 colnames(t_stats)<-c("variable", "group1", "group2", "p.adj", "p.signif", "Method")
@@ -96,10 +96,8 @@ server <- function(input, output) {
                 colnames(t_maps$label)<-c("x", "y")
                 t_maps[["brackets"]]<-as.data.frame(matrix(nrow = 0, ncol=4))
                 colnames(t_maps$brackets)<-c("y1", "y2", "x1", "x2")
-            }
-            
-            set.seed(123)
-            if (input$positive == T){
+                dades$stats<<-t_stats
+            }else{
               if (input$test == "T-test (adj Holm)"){
                 t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest")
               }
@@ -111,20 +109,23 @@ server <- function(input, output) {
               t_stats<-t_stats %>% filter(p.signif != "ns")
               
               t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups")
-              
-              ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), 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 = `.`))+
-                  # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
-                  geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0)+
-                  geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+
-                  # geom_quasirandom(position = position_quasirandom(), shape=21)+
-                  scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
-                  geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
-                  geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
-                  theme_bw()+
-                  theme(axis.text.x=element_text(angle=45, hjust=1))
+            }
+            
+            set.seed(123)
+            if (input$positive == T){
+                ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), 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 = `.`))+
+                    # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
+                    geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0)+
+                    geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+
+                    # geom_quasirandom(position = position_quasirandom(), shape=21)+
+                    scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
+                    geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
+                    geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
+                    theme_bw()+
+                    theme(axis.text.x=element_text(angle=45, hjust=1))
             }else{
                 ids<-if(ctrl %in% colnames(t_substr)){c("Mice", ctrl, "Groups")}else{c("Mice", "Groups")}
                 ggplot(melt(t_substr, id=ids), aes(variable, value))+