library(readxl)
library(tidyr)
library(dplyr)
library(ggplot2)
library(tidyverse)
library(svglite)
library(lubridate)
library(stringr)


# ACETOSA_S2_GRONOSTAJOWA_SHORT

data_gron_a_s2 <- read.table(  
  file = "X:/My Drive/staz_UJ/Rumex manuscript data analysis/Gronostajowa/tabela_gronostajowa_acetosa_s2.tsv",  
  sep = '\t', header = TRUE, na.strings = "NA", check.names = FALSE  
)  

data_filtered <- data_gron_a_s2 %>%  
  filter(sex != "0", name != "A099") %>%  
  mutate(  
    sex = as.character(sex),  
    name = as.character(name)  
  ) %>%  
  arrange(sex, desc(name)) %>%  
  mutate(across(starts_with("2020") | starts_with("2021"), as.character))  

data_long <- data_filtered %>%  
  select(name, sex, starts_with("2020"), starts_with("2021")) %>%  
  pivot_longer(  
    cols = starts_with("2020") | starts_with("2021"),  
    names_to = "date",  
    values_to = "value"  
  ) %>%  
  filter(str_sub(date, 1, 10) <= "2021.06.23") %>%  
  arrange(sex, desc(name)) %>%  
  mutate(y_axis = factor(paste(sex, name), levels = unique(paste(sex, name))))  

data_long <- data_long %>%  
  mutate(  
    value = factor(value, levels = c(  
      "w",        # winter  
      "l",        # leaves  
      "fm1", "fm2",   # male flowering  
      "ff1", "ff2",   # female flowering  
      "p1", "p2",     # pollination  
      "s1", "s2",     # seed production  
      "y"             # senescing  
    ))  
  )  

date_breaks <- c(  
  "2020.10.20-2021.04.01 winter", "2021.04.02", "2021.04.08", "2021.04.16",  
  "2021.04.23", "2021.04.29", "2021.05.03", "2021.05.07", "2021.05.10",  
  "2021.05.12", "2021.05.17", "2021.05.21", "2021.05.24", "2021.05.28",  
  "2021.06.02", "2021.06.07", "2021.06.11", "2021.06.14", "2021.06.16",  
  "2021.06.18", "2021.06.21", "2021.06.23", "2021.06.23 inflorescence cut"  
)  

tabela_gronostajowa_acetosa_s2 <- ggplot(data_long, aes(x = date, y = y_axis)) +  
  geom_tile(aes(fill = value), color = "darkslategray", width = 1, height = 1) +  
  scale_fill_manual(  
    values = c(  
      "w" = "orange2",  
      "l" = "limegreen",  
      "fm1" = "cyan", "fm2" = "cyan",  
      "ff1" = "lightskyblue1", "ff2" = "lightskyblue1",  
      "p1" = "yellow1", "p2" = "yellow1",  
      "s1" = "plum2", "s2" = "plum2",  
      "y" = "goldenrod4"  
    ),  
    name = "Legend",  
    labels = c(  
      "w" = "winter",  
      "l" = "leaves",  
      "fm1" = "male flowering", "fm2" = "male flowering",  
      "ff1" = "female flowering", "ff2" = "female flowering",  
      "p1" = "pollination", "p2" = "pollination",  
      "s1" = "seed production", "s2" = "seed production",  
      "y" = "senescing"  
    ),  
    na.value = "white"  
  ) +  
  scale_x_discrete(  
    position = "top",  
    breaks = date_breaks  
  ) +  
  theme_minimal() +  
  theme(  
    axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0, size = 30, color = "black"),  
    axis.text.x.top = element_text(angle = 90, hjust = 0, vjust = 0, size = 30, color = "black"),  
    axis.text.x.bottom = element_blank(),  
    axis.text.y = element_text(size = 30, color = "black"),  
    panel.grid = element_blank(),  
    axis.title = element_blank(),  
    legend.position = "right",  
    legend.title = element_text(size = 40, face = "bold", color = "black"),  
    legend.text = element_text(size = 30, color = "black"),  
    legend.background = element_rect(fill = "white", color = "white"),  
    legend.box.background = element_rect(fill = "white", color = "black", size = 1),  
    legend.box.margin = margin(10, 10, 10, 10)  
  ) +  
  labs(fill = "Wartość")  

ggsave("tabela_gronostajowa_acetosa_s2.png", plot = tabela_gronostajowa_acetosa_s2, width = 50, height = 20, limitsize = FALSE)  
ggsave("tabela_gronostajowa_acetosa_s2.svg", plot = tabela_gronostajowa_acetosa_s2, width = 50, height = 20, limitsize = FALSE)

# THYRSIFLORUS_S2_GRONOSTAJOWA_SHORT

data_gron_t_s2 <- read.table(  
  file = "X:/My Drive/staz_UJ/Rumex manuscript data analysis/Gronostajowa/tabela_gronostajowa_thyrsiflorus_s2.tsv",  
  sep = '\t', header = TRUE, na.strings = "NA", check.names = FALSE  
)  

data_filtered <- data_gron_t_s2 %>%  
  filter(sex != "0") %>%  
  mutate(  
    sex = as.character(sex),  
    name = as.character(name)  
  ) %>%  
  arrange(sex, desc(name)) %>%  
  mutate(across(starts_with("2020") | starts_with("2021"), as.character))  

data_long <- data_filtered %>%  
  select(name, sex, starts_with("2020"), starts_with("2021")) %>%  
  pivot_longer(  
    cols = starts_with("2020") | starts_with("2021"),  
    names_to = "date",  
    values_to = "value"  
  ) %>%  
  filter(str_sub(date, 1, 10) <= "2021.06.23") %>%  
  arrange(sex, desc(name)) %>%  
  mutate(y_axis = factor(paste(sex, name), levels = unique(paste(sex, name))))  

data_long <- data_long %>%  
  mutate(  
    value = factor(value, levels = c(  
      "w",        # winter  
      "l",        # leaves  
      "fm1", "fm2",   # male flowering  
      "ff1", "ff2",   # female flowering  
      "p1", "p2",     # pollination  
      "s1", "s2",     # seed production  
      "y"             # senescing  
    ))  
  )  

date_breaks <- c(  
  "2020.10.20-2021.04.01 winter", "2021.04.02", "2021.04.08", "2021.04.16",  
  "2021.04.23", "2021.04.29", "2021.05.03", "2021.05.07", "2021.05.10",  
  "2021.05.12", "2021.05.17", "2021.05.21", "2021.05.24", "2021.05.28",  
  "2021.06.02", "2021.06.07", "2021.06.11", "2021.06.14", "2021.06.16",  
  "2021.06.18", "2021.06.21", "2021.06.23", "2021.06.23 inflorescence cut"  
)  

tabela_gronostajowa_thyrsiflorus_s2 <- ggplot(data_long, aes(x = date, y = y_axis)) +  
  geom_tile(aes(fill = value), color = "darkslategray", width = 1, height = 1) +  
  scale_fill_manual(  
    values = c(  
      "w" = "orange2",  
      "l" = "limegreen",  
      "fm1" = "cyan", "fm2" = "cyan",  
      "ff1" = "lightskyblue1", "ff2" = "lightskyblue1",  
      "p1" = "yellow1", "p2" = "yellow1",  
      "s1" = "orchid1", "s2" = "orchid1",  
      "y" = "goldenrod4"  
    ),  
    name = "Legend",  
    labels = c(  
      "w" = "winter",  
      "l" = "leaves",  
      "fm1" = "male flowering", "fm2" = "male flowering",  
      "ff1" = "female flowering", "ff2" = "female flowering",  
      "p1" = "pollination", "p2" = "pollination",  
      "s1" = "seed production", "s2" = "seed production",  
      "y" = "senescing"  
    ),  
    na.value = "white"  
  ) +  
  scale_x_discrete(  
    position = "top",  
    breaks = date_breaks  
  ) +  
  theme_minimal() +  
  theme(  
    axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0, size = 30, color = "black"),  
    axis.text.x.top = element_text(angle = 90, hjust = 0, vjust = 0, size = 30, color = "black"),  
    axis.text.x.bottom = element_blank(),  
    axis.text.y = element_text(size = 30, color = "black"),  
    panel.grid = element_blank(),  
    axis.title = element_blank(),  
    legend.position = "right",  
    legend.title = element_text(size = 40, face = "bold", color = "black"),  
    legend.text = element_text(size = 30, color = "black"),  
    legend.background = element_rect(fill = "white", color = "white"),  
    legend.box.background = element_rect(fill = "white", color = "black", size = 1),  
    legend.box.margin = margin(10, 10, 10, 10)  
  ) +  
  labs(fill = "Wartość")  

ggsave("tabela_gronostajowa_thyrsiflorus_s2.png", plot = tabela_gronostajowa_thyrsiflorus_s2, width = 50, height = 20, limitsize = FALSE)  
ggsave("tabela_gronostajowa_thyrsiflorus_s2.svg", plot = tabela_gronostajowa_thyrsiflorus_s2, width = 50, height = 20, limitsize = FALSE)