diff --git a/app.R b/app.R index 285c237..6babe04 100644 --- a/app.R +++ b/app.R @@ -122,17 +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$stats<<-null @@ -148,7 +144,7 @@ server <- function(input, output) { need(exists("mock_mean"), "No se puede elegir positividad con mĂșltiples mocks") ) if (exists("mock_mean")){ - ggplot(melt(t_substr, id=ids), aes(variable, value))+ + g<-ggplot(melt(t_substr, id=ids), aes(variable, value))+ labs(x="", y="Spots/2.5*10^5 cells")+ # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+ geom_hline(data=mock_mean, aes(color=Groups, yintercept = `.`))+ @@ -165,7 +161,7 @@ server <- function(input, output) { }else{ ids=c("Mice", "Groups", c(ctrl, mock)[c(ctrl, mock) %in% colnames(t_substr)]) - ggplot(melt(t_substr, id=ids), aes(variable, value))+ + g<-ggplot(melt(t_substr, id=ids, variable.name = "Condition"), aes(Condition, value))+ labs(x="", y="Spots/2.5*10^5 cells")+ # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+ # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+ @@ -173,11 +169,17 @@ server <- function(input, output) { geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+ # geom_quasirandom(width=0.2, position=position_dodge(), shape=21)+ scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+ - geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+ - geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), 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$y, label=p.signif), color="black")+ theme_bw()+ theme(axis.text.x=element_text(angle=45, hjust=1)) } + if (input$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 + } } }) @@ -207,12 +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_maps<-dades$maps - + t_stats<-dades$stats + 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`)+ @@ -227,13 +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)+