per_patient_analysis

print_tab <- function(plt,title) {
   cat("## ",title,"{.unnumbered }"," \n")
  print(
    plt
    )
  plot.new()
  dev.off()
  cat(' \n\n')
}

1 All cells combined

---

lung = SetIdent(object = lung,value = "program.assignment")
lung  = RenameIdents(object = lung,"metagene.1" = "Hypoxia")
lung  = RenameIdents(object = lung,"metagene.2" = "TNFa")
lung  = RenameIdents(object = lung,"metagene.1" = "cell_cycle")

Error in RenameIdents.Seurat(object = lung, metagene.1 = "cell_cycle") : 
  Cannot find any of the provided identities

 df  = FetchData(object = lung,vars = c("program.assignment","time.point")) %>% 
    filter (program.assignment %in% c("Hypoxia","TNFa")) %>% 
    filter (time.point %in% c("pre-treatment","on-treatment")) %>% 
    droplevels() 
  test = fisher.test(table(df))
    
  library(ggstatsplot)
print(
    ggbarstats(
    df, program.assignment, time.point,
    results.subtitle = FALSE,
    subtitle = paste0(
      "Fisher's exact test", ", p-value = ",
      ifelse(test$p.value < 0.001, "< 0.001", round(test$p.value, 3))
    )
  )
)

cell_percentage(dataset = lung,time.point_var = "time.point")

2 Per patient fisher test

---

patients_vector = lung$patient.ident %>% unique()
for (patient_name in patients_vector) {
  df  = FetchData(object = lung,vars = c("program.assignment","patient.ident","time.point")) %>% 
    filter (patient.ident == patient_name) %>% 
    filter (program.assignment %in% c("Hypoxia","TNFa")) %>% 
    filter (time.point %in% c("pre-treatment","on-treatment")) %>% 
    select(-patient.ident) %>% 
    droplevels() 
  test = fisher.test(table(df))
    
  library(ggstatsplot)

   p =  ggbarstats(
    df, program.assignment, time.point,
    results.subtitle = FALSE,
    subtitle = paste0(
      "Fisher's exact test", ", p-value = ",
      ifelse(test$p.value < 0.001, "< 0.001", round(test$p.value, 3))
    ),title = patient_name
  )
print_tab(plt = p,title = patient_name)
}

X1071

X1144

X1167

MGH088

MGH1066

X1155

NA

3 Per patient programs ratio

---

cell_percentage = function(dataset,time.point_var) {
    data =FetchData(object = dataset,vars = c("program.assignment",time.point_var))
  data = data %>% dplyr::count(program.assignment, .[time.point_var]) %>%  dplyr::add_count(program.assignment, wt = n, name = "overall")%>% 
  mutate(proportion = n / overall)   
  
  plt_list = list()
    time.point_var = ensym(time.point_var)
  for (program_name in unique(data$program.assignment)) {
    program_data = data[data$program.assignment == program_name,]
    p = ggplot(data=program_data, aes(x=!!time.point_var, y=proportion)) +geom_bar(stat="identity")+ylab("precentage") +
      ggtitle("program" %>% paste(program_data$program.assignment %>% unique() %>% as.character()))+
      scale_y_continuous(limits = c(0,1))   
      plt_list[[program_name]] = p
  }
  p = ggarrange(plotlist = plt_list )

  return(p)
}

patients_vector = lung$patient.ident %>% unique()
for (patient_name in patients_vector) {
  patient_data = subset(x = lung, subset = patient.ident == patient_name)
  print_tab(plt = cell_percentage(dataset = patient_data,time.point_var = "time.point"),title = patient_name)

}

X1071

X1144

X1167

MGH088

MGH1066

X1155

NA

NA