diff --git a/app.R b/app.R index 660ef66..29e6da2 100644 --- a/app.R +++ b/app.R @@ -52,19 +52,32 @@ server <- function(input, output) { table<-dades$taula[,colnames(dades$taula) != "Groups"] t_mean<-dcast(melt(table, id="Mice"),Mice~variable, mean, na.rm=T) - t_substr<-data.frame("Mice"=t_mean[,1], - as.data.frame(t(apply(t_mean[,2:ncol(table)], 1, function(x) x-x[mock]))) - ) - t_mean_group<-merge(t_mean, unique(dades$taula[c("Mice","Groups")]), id="Mice") - mock_mean<-dcast(t_mean_group, Groups~., value.var=mock, mean) - mock_mean[,2]<-mock_mean[,2]*2 - mock_mean[mock_mean$. < input$umbral_pos,2]<-input$umbral_pos - - t_substr<-merge(t_substr, unique(dades$taula[c("Mice","Groups")]), id="Mice") - t_substr<-t_substr[,c(1, ncol(t_substr), 2:(ncol(t_substr)-1))] - t_substr<-t_substr[,c("Mice", "Groups", colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")])] - t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0)) - colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)]) + if (length(grep("Mock", colnames(t_mean))) == 1){ + t_substr<-data.frame("Mice"=t_mean[,1], + as.data.frame(t(apply(t_mean[,2:ncol(table)], 1, function(x) x-x[mock]))) + ) + t_mean_group<-merge(t_mean, unique(dades$taula[c("Mice","Groups")]), id="Mice") + t_mean_group$Groups<-as.factor(t_mean_group$Groups) + mock_mean<-dcast(t_mean_group, Groups~., value.var=mock, mean) + mock_mean[,2]<-mock_mean[,2]*2 + mock_mean[mock_mean$. < input$umbral_pos,2]<-input$umbral_pos + + t_substr<-merge(t_substr, unique(dades$taula[c("Mice","Groups")]), id="Mice") + t_substr<-t_substr[,c(1, ncol(t_substr), 2:(ncol(t_substr)-1))] + t_substr<-t_substr[,c("Mice", "Groups", colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")])] + t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0)) + colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)]) + }else{ + print(1) + t_especifica<-t_mean[,grep("Mock_", colnames(t_mean), invert=T)] + t_mock<-t_mean[,c(which(colnames(t_mean) == "Mice"),grep("Mock_", colnames(t_mean)))] + t_temp<-melt(t_especifica, variable.name = "condition", value.name = "spots") + t_temp["spots_mock"]<-melt(t_mock, variable.name = "condition")[,"value"] + t_substr<-data.frame(t_temp[c("Mice","condition")], "spots"=t_temp["spots"]-t_temp["spots_mock"]) + t_substr<-dcast(t_substr, Mice~condition) + t_substr<-merge(t_substr, unique(dades$taula[c("Mice","Groups")]), id="Mice") + t_substr$Groups<-as.factor(t_substr$Groups) + } t_substr_gp<-t_substr t_substr_gp[3:ncol(t_substr)]<-apply(t_substr[3:ncol(t_substr)], 2, function(x) gsub(".",",",x, fixed=T)) @@ -74,17 +87,6 @@ server <- function(input, output) { write.xlsx(doc, "data4graphpad.xlsx",rowNames=T) t<-melt(t_substr[,!colnames(t_substr) %in% c(ctrl, mock)]) - if (input$test == "T-test (adj Holm)"){ - t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest") - } - if (input$test == "Wilcoxon (adj Holm)"){ - t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "wilcox") - } - - dades$stats<<-t_stats - t_stats<-t_stats %>% filter(p.signif != "ns") - - t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups") if (input$showstats == F){ t_stats<-as.data.frame(matrix(nrow=0, ncol=6)) @@ -98,21 +100,34 @@ server <- function(input, output) { set.seed(123) if (input$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$y, label=p.signif), color="black")+ - theme_bw()+ - theme(axis.text.x=element_text(angle=45, hjust=1)) + if (input$test == "T-test (adj Holm)"){ + t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest") + } + if (input$test == "Wilcoxon (adj Holm)"){ + t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "wilcox") + } + + dades$stats<<-t_stats + 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)) }else{ - ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+ + ids<-if(ctrl %in% colnames(t_substr)){c("Mice", ctrl, "Groups")}else{c("Mice", "Groups")} + 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_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+