diff --git a/invivos/app.R b/invivos/app.R index 6f246d1..c848b97 100755 --- a/invivos/app.R +++ b/invivos/app.R @@ -374,30 +374,7 @@ server <- function(input, output) { oneside<-"" table<-analysis$taula - if ("ID.animal" %in% colnames(table)){table<-rename(table, "ID animal"=`ID.animal`)} - if ("ID" %in% colnames(table)){table<-rename(table, "ID animal"=ID)} - if ("ID.tumor" %in% colnames(table)){table<-rename(table, "ID tumor"=`ID.tumor`)} - # table[table$ID.tumor == "R","0"]<-NA - col_nodays<-c("ID","Code", "Cage","Group", "ID.animal","ID animal", "ID.tumor", "ID tumor", "TS","DPV", "Absorbance") - if (length(grep(0, colnames(table)[!colnames(table) %in% col_nodays])) == 0 & input$vacc == "Sí"){ - table["0"]<-0 - } - table<-melt(table, id=colnames(table)[colnames(table) %in% col_nodays], variable.name = "Timepoint") - table$Timepoint<-gsub("[A-Za-z ]","",table$Timepoint) - # print(table) - if ("DPV" %in% colnames(table)){ - table<-dcast(table, Cage+`ID animal`+`ID tumor`+Group+Timepoint~DPV, value.var = "value") - table$Major<-table$Major - table$Minor<-table$Minor - table["Volume"]<-((table$Major*table$Minor*table$Minor)*(pi/6)) - } - if ("TS" %in% colnames(table)){ - table<-dcast(table, Cage+`ID animal`+`ID tumor`+Group+Timepoint~TS, value.var = "value") - table["Volume"]<-table$`TS-Deep`*table$`TS-Length`*table$`TS-Width`*pi/6 - } - if (!"Volume" %in% colnames(table)){table<-rename(table, "Volume"=value)} table<-table %>% filter(!is.na(Group)) - table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint))))) if (input$increase_volume){ timepoints<-unique(table$Timepoint) table<-table %>% select(-Major, -Minor) %>% @@ -406,11 +383,7 @@ server <- function(input, output) { gather(Timepoint, Volume, -Cage, -`ID animal`, -`ID tumor`, -Group) %>% mutate(Volume=case_when(Volume < 0 ~ 0, T~Volume)) } - table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint))))) - analysis$taula_def<-table - analysis$taula_vol<-dcast(table, Cage+`ID animal`+`ID tumor`~Timepoint,value.var = "Volume") - table_plot<-dcast(dcast(table %>% filter(!is.na(Volume)), `ID animal`+Group+Timepoint~., value.var = "Volume", fun.aggregate = mean), Group~Timepoint) - table_plot + table %>% group_by(Group, DayPostInoc, Side) %>% count() %>% spread(DayPostInoc, n) } }) output$cin_group<-renderPlot({