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library(tidyverse)
library(scales)
library(fabricatr)      # to fabricate fake data
library(glue)           # to prepare label text
library(broom)          # to tidy prop.test()
library(lemon)          # for facet_rep_wrap() function


theme_set(theme_light(base_family = "IBM Plex Sans"))

# FLOT
set.seed(2022)
FLOT_intestinal <- fabricate(
  N = 52,
  main_group = "FLOT",
  lauren = "intestinal",
  response = c(rep("1a", 12), rep("1b", 10), rep("others", N-22)))

FLOT_mixed <- fabricate(
  N = 11,
  main_group = "FLOT",
  lauren = "mixed",
  response = c(rep("1a", 0), rep("1b", 5), rep("others", N-5)))

FLOT_diffuse <- fabricate(
  N = 34,
  main_group = "FLOT",
  lauren = "diffuse",
  response = c(rep("1a", 1), rep("1b", 7), rep("others", N-8)))


# ECF/ECX
set.seed(2022)
ECF_intestinal <- fabricate(
  N = 60,
  main_group = "ECF/ECX",
  lauren = "intestinal",
  response = c(rep("1a", 6), rep("1b", 8), rep("others", N-14)))

ECF_mixed <- fabricate(
  N = 7,
  main_group = "ECF/ECX",
  lauren = "mixed",
  response = c(rep("1a", 1), rep("1b", 0), rep("others", N-1)))

ECF_diffuse <- fabricate(
  N = 39,
  main_group = "ECF/ECX",
  lauren = "diffuse",
  response = c(rep("1a", 1), rep("1b", 9), rep("others", N-10)))

# Combine datasets
combined_dataset <- bind_rows(
  FLOT_intestinal, FLOT_mixed, FLOT_diffuse,
  ECF_intestinal, ECF_mixed, ECF_diffuse,
) %>% 
  mutate(ID = paste0("p_" ,row_number()), .before = "main_group") %>% 
  as_tibble()

set.seed(2022)
combined_dataset %>% 
  sample_n(10)

tidy_data <- combined_dataset %>% 
  group_by(main_group, lauren) %>% 
  summarise(n = n(),
            n_1a = sum(response == "1a"),
            n_1a1b = sum(response == "1a" | response == "1b")) %>% 
  ungroup() %>% 
  pivot_longer(cols = c("n_1a", "n_1a1b"),
               names_to = "facet_group",
               values_to = "values") %>% 
  rowwise() %>% 
  mutate(prop_table = list(tidy(prop.test(values, n, conf.level=0.95)))) %>% 
  unnest(prop_table) %>% 
  mutate(estimate = estimate * 100,
         conf.low = conf.low * 100,
         conf.high = conf.high * 100) %>%                   # mutate_at() or mutate(across()) is possible.
  select(main_group:estimate, conf.low, conf.high) %>%      # just to simplify the dataset
  mutate_at(c("main_group", "lauren", "facet_group"), factor) %>% 
  mutate(main_group = fct_relevel(main_group, c("FLOT")),
         lauren = fct_relevel(lauren, c("intestinal", "mixed", "diffuse"))) %>% 
  mutate(label_text = if_else(values == 0, glue("{values}/{n}"), glue("{values}/{n} \n({round(estimate)}%)")))

final_replica <- tidy_data %>% 
  ggplot(aes(lauren, estimate, fill = main_group)) +
  geom_col(position = "dodge", colour="black", width = .7) +
  geom_errorbar(aes(ymax = conf.high, ymin = conf.low), position = position_dodge(width = .7), width = .15) +
  facet_rep_wrap(~ facet_group, ncol = 1,  strip.position = "left",  labeller = as_labeller(c(n_1a = "Patients with TRG1a (%)", n_1a1b = "Patients with TRG1a/b (%)"))) +
  scale_y_continuous(limits = c(-2, 100), breaks = seq(0,100,10), expand = c(0, 0)) + # -2 was used to add outside ticks
  scale_x_discrete(labels = c("Intestinal", "Mixed",  "Diffuse")) +
  scale_fill_manual(values =  c("#D8A09A", "#9ED0D9")) +
  geom_text(aes(y = conf.high + 8, label = label_text), position = position_dodge(width = .7), size = 4, family = "IBM Plex Sans") + 
  geom_hline(yintercept = 0, color = "black", size = .5) +
  labs(y = "",
       x = "Lauren's classification",
       fill = "") +
  theme(plot.margin = unit(c(.5, .5, .5, 0), "cm"),
        plot.background = element_rect(colour = "#BC687F", fill = NA, size = .5),
        strip.placement = "outside",
        strip.background = element_blank(),
        strip.text = element_text(color = "black", size = 11),
        panel.grid = element_blank(),
        panel.border = element_blank(),
        panel.spacing = unit(1, "cm"),
        axis.line = element_line(color = "black"),
        axis.line.x = element_blank(),
        axis.ticks.y = element_line(color = "black", size = .5),
        axis.ticks.length.y = unit(.2, "cm"),
        axis.text.y = element_text(size = 11, color = "black"),
        axis.text.x = element_text(size = 11, color = "black"),
        axis.title.x = element_text(vjust = -1.5),
        legend.position = c(.85, .95),
        legend.text = element_text(size = 12),
        legend.key.height= unit(.4, "cm"),
        legend.spacing.y = unit(.25, "cm"),
        axis.ticks.x = element_blank()) +
  guides(fill = guide_legend(byrow = TRUE)) +
  geom_segment(aes(x = 1.5, xend = 1.5, y = 0, yend = -2)) +
  geom_segment(aes(x = 2.5, xend = 2.5, y = 0, yend = -2)) +
  geom_segment(aes(x = 3.5, xend = 3.5, y = 0, yend = -2)) 


### SAVE FIGURE
ggsave(final_replica,
       file =file.path ("w7_replica.jpg"),
       dpi = 300,
       width = 6,
       height = 9)