diff --git a/invivos/app.R b/invivos/app.R index 1b08f06..309527d 100755 --- a/invivos/app.R +++ b/invivos/app.R @@ -587,6 +587,20 @@ server <- function(input, output) { observeEvent(analysis$taula, {}) table<-analysis$taula if (input$vacc == "Sí"){ + firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% + select(DayPostInoc, Side) %>% unique() %>% + group_by(Side) %>% summarise(FirstOper=min(DayPostInoc)) + if (input$operated == TRUE){ + for (i in 1:nrow(firstoper)){ + table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i]) + } + }else{ + if(input$dead == TRUE){ + deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% + pull(Animal) + table<-table %>% filter(!Animal %in% deadmice) + } + } g<-list() for (side in c("L","R")){ tableR<-filter(table, Side == side) %>% filter(!is.na(Volume)) @@ -594,7 +608,7 @@ server <- function(input, output) { endtime["Dead"]<-dcast(tableR, Cage+Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff table_tumor<<-endtime - g[side]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor), + g[side]<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor), pval = T, pval.method = T, title = side, # legend.labs = paste(c("< median", ">= median"), "MICA"), @@ -613,13 +627,27 @@ server <- function(input, output) { do.call(grid.arrange, g) }else{ + firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% + pull(DayPostInoc) %>% min(na.rm = T) + print(firstoper) + + if (input$operated == TRUE){ + table<-table %>% filter(DayPostInoc < firstoper) + }else{ + deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% + pull(Animal) + if(input$dead == TRUE){ + table<-table %>% filter(!Animal %in% deadmice) + } + } + tableR<-table %>% filter(!is.na(Volume)) endtime<-dcast(if(length(unique(tableR$DayPostInoc)) > 1){tableR %>% filter(Volume < input$cutoff)}else{tableR}, Animal+Side+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime["Dead"]<-dcast(tableR, Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") >= input$cutoff table_tumor<<-endtime - g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor), + g<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor), pval = T, pval.method = T, # legend.labs = paste(c("< median", ">= median"), "MICA"), ggtheme=theme_classic(base_size=15) @@ -901,6 +929,20 @@ server <- function(input, output) { } if (input$vacc == "Sí"){ + firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% + select(DayPostInoc, Side) %>% unique() %>% + group_by(Side) %>% summarise(FirstOper=min(DayPostInoc)) + if (input$operated == TRUE){ + for (i in 1:nrow(firstoper)){ + table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i]) + } + }else{ + if(input$dead == TRUE){ + deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% + pull(Animal) + table<-table %>% filter(!Animal %in% deadmice) + } + } g<-list() count<-1 for (side in c("L","R")){ @@ -914,7 +956,7 @@ server <- function(input, output) { col<-gg_color_hue(length(unique(endtime$Group))) } table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group)) - g[[count]]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor), + g[[count]]<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor), pval = T, pval.method = T, title = side, ggtheme=theme_classic(base_size=input$`font-size`), @@ -925,6 +967,19 @@ server <- function(input, output) { g_surv_vacc<-g }else{ + firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% + pull(DayPostInoc) %>% min(na.rm = T) + print(firstoper) + + if (input$operated == TRUE){ + table<-table %>% filter(DayPostInoc < firstoper) + }else{ + deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>% + pull(Animal) + if(input$dead == TRUE){ + table<-table %>% filter(!Animal %in% deadmice) + } + } tableR<-table %>% filter(!is.na(Volume)) endtime<-dcast(tableR %>% filter(Volume < (input$cutoff*as.numeric(input$unit_fact))), Animal+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime["Dead"]<-dcast(tableR, Animal+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > (input$cutoff*as.numeric(input$unit_fact)) @@ -935,7 +990,7 @@ server <- function(input, output) { col<-gg_color_hue(length(unique(table_tumor$Group))) } table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group)) - g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor), + g<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor), pval = T, pval.method = T, # ggtheme=theme_classic(base_size=input$`font-size`), palette = col