---
title: "dlugosc_kwitnienia"
output: 
  html_document: default
always_allow_html: true
date: "2025-03-05"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(kableExtra)
library(ggplot2)

```

Data: 
`flowering.tsv`

```{r read_data, echo=FALSE}
data_file <- "flowering.tsv"
data <- read.table(file=paste(data_file), sep = '\t', header = TRUE,  na.strings = "NA")
#print(data)
```


## Flowering time

```{r flowering-sel_danych, echo=FALSE}
# R. acetosa, męskie
am <- data[data$species == 'R. acetosa' & data$sex == 'M', ]
# R. acetosa, żeńskie
af <- data[data$species == 'R. acetosa' & data$sex == 'F', ]
# Analogicznie, R. thyrsiflorus
tm <- data[data$species == 'R. thyrsiflorus' & data$sex == 'M', ]
tf <- data[data$species == 'R. thyrsiflorus' & data$sex == 'F', ]
```

```{r functions, echo=FALSE}
describe_flowering <- function(df, species, sex, dat_all, kol) {
  dat = dat_all[, kol]
  tt = t.test(dat)
  df <- rbind(df, data.frame(
                 species = species,
                 sex = sex,
                 min = min(dat),
                 max = max(dat),
                 mean = round(mean(dat), 2),
                 sd = round(sd(dat), 2),
                 ci_min = round(tt$conf.int[1], 2),
                 ci_max = round(tt$conf.int[2], 2)
                 ))
  return(df)
}

compare_flowering <- function(df, species1, species2, sex1, sex2,
                              dat1_all, dat2_all, kol) {
  dat1 = dat1_all[, kol]
  dat2 = dat2_all[, kol]
  tt = t.test(dat1, dat2)
  df <- rbind(df, data.frame(
                 species1 = species1,
                 species2 = species2,
                 sex1 = sex1,
                 sex2 = sex2,
                 set1_mean = round(mean(dat1), 2),
                 set2_mean = round(mean(dat2), 2),
                 means_difference = round((mean(dat1) - mean(dat2)), 2),
                 p_val = round(tt$p.value, 6),
                 ci_min = round(tt$conf.int[1], 2),
                 ci_max = round(tt$conf.int[2], 2)))
  return(df)
}
```

## First flowering - description 
```{r flowering-opis, echo=FALSE}
flowering1_desc <- data.frame(
                 species = character(),
                 sex = character(),
                 min = numeric(),
                 max = numeric(),
                 mean = numeric(),
                 sd = numeric(),
                 ci_min = numeric(),
                 ci_max = numeric(),
                 stringsAsFactors = FALSE)

flowering1_desc <- describe_flowering(flowering1_desc, "R. acetosa", "M", am, "sum_1")
flowering1_desc <- describe_flowering(flowering1_desc, "R. acetosa", "F", af, "sum_1")
flowering1_desc <- describe_flowering(flowering1_desc, "R. thyrsiflorus", "M", tm, "sum_1")
flowering1_desc <- describe_flowering(flowering1_desc, "R. thyrsiflorus", "F", tf, "sum_1")


knitr::kable(flowering1_desc) %>% kable_styling(full_width = FALSE, position = "center")
write.table(flowering1_desc, file = "flowering1_desc.tsv", 
            sep = "\t",           
            row.names = FALSE,    
            quote = FALSE,        
            na = "NA")
```

## First flowering - comparisons
```{r flowering-comp, echo=FALSE}
flowering1_comp <- data.frame(
                 species1 = character(),
                 species2 = character(),
                 sex1 = character(),
                 sex2 = character(),
                 set1_mean = numeric(),
                 set2_mean = numeric(),
                 means_difference = numeric(),
                 p_val = numeric(),
                 ci_min = numeric(),
                 ci_max = numeric(),
                 stringsAsFactors = FALSE)

flowering1_comp <- compare_flowering(flowering1_comp, "R. acetosa", "R. acetosa", 
                                     "M", "F", am, af, "sum_1")
flowering1_comp <- compare_flowering(flowering1_comp, "R. thyrsiflorus", "R. thyrsiflorus", 
                                     "M", "F", tm, tf, "sum_1")
flowering1_comp <- compare_flowering(flowering1_comp, "R. acetosa", "R. thyrsiflorus", 
                                     "M", "M", am, tm, "sum_1")
flowering1_comp <- compare_flowering(flowering1_comp, "R. acetosa", "R. thyrsiflorus", 
                                     "F", "F", af, tf, "sum_1")


knitr::kable(flowering1_comp) %>% kable_styling(full_width = FALSE, position = "center")

write.table(flowering1_comp, file = "flowering1_comp.tsv", 
            sep = "\t",           
            row.names = FALSE,    
            quote = FALSE,        
            na = "NA")
```




```{r rozklady, echo=FALSE}
data$name <- paste(data$species, data$sex, sep='')
flowering1_desc$name <- paste(flowering1_desc$species,  flowering1_desc$sex, sep='')
p <- ggplot(data = data) +
  geom_jitter(mapping = aes(x = name, y = sum_1, fill = sex),
              shape=21,
              stroke=1,
              position = position_jitter(width = 0.3, height = 0), 
              alpha = 0.5,
              size = 2) +
  geom_point(data = flowering1_desc, aes(x = name, y = mean),
                position = position_dodge(width = 0.5), size = 4) +
  geom_errorbar(data = flowering1_desc, aes(x = name, ymin = ci_min, 
                                             ymax = ci_max),
                    width = 0.2, position = position_dodge(width = 0.5)) +
  scale_fill_manual(values = c("M" = "black", "F" = "white")) +
  theme_minimal()


ggsave(filename = "jitter.svg", plot = p, width = 8, height = 6, dpi = 300, bg = "transparent")
ggsave(filename = "jitter.pdf", plot = p, width = 8, height = 6, bg = "transparent")
ggsave(filename = "jitter.png", plot = p, width = 8, height = 6, dpi = 300, bg = "transparent")

p


```