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95 lines
4.1 KiB
95 lines
4.1 KiB
---
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title: "Elispots"
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output: html_document
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params:
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file: "../Elispot-validation-spots.xlsx"
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positive: F
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showstats: F
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test: "Ttest"
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umbral_pos: 10
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---
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```{r, echo=F, warning=F, message=F}
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dades<-read_xlsx(params$file)
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ctrl<-"Ctrl+"
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mock<-"Mock"
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table<-dades[,colnames(dades) != "Groups"]
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t_mean<-dcast(melt(table, id="Mice"),Mice~variable, mean, na.rm=T)
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t_substr<-data.frame("Mice"=t_mean[,1],
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as.data.frame(t(apply(t_mean[,2:ncol(table)], 1, function(x) x-x[mock])))
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)
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t_mean_group<-merge(t_mean, unique(dades[c("Mice","Groups")]), id="Mice")
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mock_mean<-dcast(t_mean_group, Groups~., value.var=mock, mean)
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mock_mean[,2]<-mock_mean[,2]*2
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mock_mean[mock_mean$. < params$umbral_pos,2]<-params$umbral_pos
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t_substr<-merge(t_substr, unique(dades[c("Mice","Groups")]), id="Mice")
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t_substr<-t_substr[,c(1, ncol(t_substr), 2:(ncol(t_substr)-1))]
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t_substr<-t_substr[,c("Mice", "Groups", colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")])]
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t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0))
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colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)])
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t<-melt(t_substr[,!colnames(t_substr) %in% c(ctrl, mock)])
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if (params$test == "T-test (adj Holm)"){
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t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest")
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}
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if (params$test == "Wilcoxon (adj Holm)"){
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t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "wilcox")
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}
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t_stats<-t_stats %>% filter(p.signif != "ns")
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t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups")
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if (params$showstats == F){
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t_stats<-as.data.frame(matrix(nrow=0, ncol=6))
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colnames(t_stats)<-c("variable", "group1", "group2", "p.adj", "p.signif", "Method")
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t_maps<-list()
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t_maps[["label"]]<-as.data.frame(matrix(nrow = 0, ncol=2))
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colnames(t_maps$label)<-c("x", "y")
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t_maps[["brackets"]]<-as.data.frame(matrix(nrow = 0, ncol=4))
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colnames(t_maps$brackets)<-c("y1", "y2", "x1", "x2")
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}
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set.seed(123)
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if (params$positive == T){
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ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+
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labs(x="", y="Spots/2.5*10^5 cells")+
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geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
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geom_hline(data=mock_mean, aes(color=Groups, yintercept = `.`))+
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geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
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geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups))+
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# geom_quasirandom(position = position_quasirandom(), shape=21)+
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scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
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geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
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geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
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theme_bw()+
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theme(axis.text.x=element_text(angle=45, hjust=1))
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}else{
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ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+
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labs(x="", y="Spots/2.5*10^5 cells")+
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geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
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geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
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geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups))+
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# geom_quasirandom(width=0.2, position=position_dodge(), shape=21)+
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scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
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geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
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geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
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theme_bw()+
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theme(axis.text.x=element_text(angle=45, hjust=1))
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}
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```
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```{r, echo=F, warning=F, message=F}
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t_stats %>%
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flextable() %>%
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theme_vanilla() %>%
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fontsize(size=14, part="all") %>%
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padding(padding=10, part="all") %>%
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color(~ p.adj < 0.05, color = "red")%>%
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autofit()
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```
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