rmats-pie.Rmd

---
title: "--"
author: "rbarreiro"
date: "--"
output: 
  html_document: 
    theme: journal
    css: rmark.css
---

```{r setup, include=FALSE}
suppressMessages({
  library(tidyverse)
  library(scales)
  library(cowplot)
  library(ggbeeswarm)
  library(ggsci)
  library(viridis)
  library(knitr)
  library(ggpubr)
  library(ggrepel)
  library(eulerr)
})

theme_set(
  theme_bw() + theme(plot.title = element_text(face = "bold"))
)

options(scipen=15000000)

my_color_pal <- c(
  UP=ggsci::pal_jco()(4)[1],
  DOWN=ggsci::pal_jco()(4)[4]
)
```



```{r echo=FALSE, warning=FALSE, fig.width=3.35*1.25, fig.height=3.51*2.25}
# for (IncLevelDifference_cutoff in c(0.1, 0.15, 0.2, 0.25, 0.3)){
  
  IncLevelDifference_cutoff <- 0.2
  my_data <- data.frame()
  for (my_filename in list.files('input', full.names = TRUE, include.dirs = FALSE)){
    suppressMessages(x <- read_delim(my_filename, delim = '\t'))
    x$EventType  <- basename(my_filename) %>% str_replace(".*_(.*).MATS.*","\\1")
    x$RBP        <- basename(my_filename) %>% str_replace("_.*","")

    my_data <- bind_rows(my_data,x)
  }

  my_data_50 <- my_data %>% filter(FDR < 0.01, abs(IncLevelDifference) > IncLevelDifference_cutoff) %>% mutate(Ctl = "Ctl50")
  
  
only_ids <- 
  my_data_50 %>%  
  mutate(psi_signal = if_else(IncLevelDifference<0,'-PSI','+PSI')) %>%
  unite(chr,strand,longExonStart_0base, longExonEnd, shortES, shortEE, flankingES, flankingEE, `1stExonStart_0base`, `1stExonEnd`,
        `2ndExonStart_0base`,`2ndExonEnd`,upstreamES,upstreamEE,downstreamES,downstreamEE,riExonStart_0base,
        riExonEnd,exonStart_0base,exonEnd,psi_signal,sep = "__", col = "my_id") %>%
  select(my_id)


my_data_with_id <-
  my_data_50 %>%
  bind_cols(only_ids)

my_overlap <-
  my_data_with_id %>%
  count(my_id) %>%
  filter(n > 1) %>%
  pull(my_id)

over <-
  my_data_with_id %>%
  filter(my_id %in% my_overlap)
```

```{r}
p <-
  my_data_with_id %>%
  filter(RBP == 'U251') %>%
  count(EventType) %>% 
    mutate(n_raw = n) %>%
  mutate(n = n / sum(n)) %>%
  ggplot(aes(x="", y=n, fill=EventType)) + geom_bar(stat="identity", width=1)+
  coord_polar("y", start=0) +
  geom_label(aes(label = paste0(n_raw,"(",round(n*100), "%)")), position = position_stack(vjust = 0.5), size = 3) +
  theme_classic() + theme(axis.line = element_blank(),
          axis.text = element_blank(),
          axis.ticks = element_blank(),
          plot.title = element_text(hjust = 0.5, color = "#666666")) +
  labs(x = NULL, y = NULL, fill = NULL, title = "U251 - AS") +
  ggsci::scale_fill_locuszoom()

ggsave('U251.pdf',p)

p <- 
  my_data_with_id %>%
  filter(RBP == 'U343') %>%
  count(EventType) %>% 
  mutate(n_raw = n) %>%
  mutate(n = n / sum(n)) %>%
  ggplot(aes(x="", y=n, fill=EventType)) + geom_bar(stat="identity", width=1)+
  coord_polar("y", start=0) +
  geom_label(aes(label = paste0(n_raw,"(",round(n*100), "%)")), position = position_stack(vjust = 0.5), size = 3) +
  theme_classic() + theme(axis.line = element_blank(),
          axis.text = element_blank(),
          axis.ticks = element_blank(),
          plot.title = element_text(hjust = 0.5, color = "#666666")) +
  labs(x = NULL, y = NULL, fill = NULL, title = "U343 - AS") +
  ggsci::scale_fill_locuszoom()

ggsave('U343.pdf', p)


p <-
  my_data_with_id %>%
  filter(my_id %in% my_overlap) %>%
  filter(RBP == 'U251') %>%
  count(EventType) %>% 
  mutate(n_raw = n) %>%
  mutate(n = n / sum(n)) %>%
  ggplot(aes(x="", y=n, fill=EventType)) + geom_bar(stat="identity", width=1)+
  coord_polar("y", start=0) +
  geom_label(aes(label = paste0(n_raw,"(",round(n*100), "%)")), position = position_stack(vjust = 0.5), size = 3) +
  theme_classic() + theme(axis.line = element_blank(),
          axis.text = element_blank(),
          axis.ticks = element_blank(),
          plot.title = element_text(hjust = 0.5, color = "#666666")) +
  labs(x = NULL, y = NULL, fill = NULL, title = "Overlap - AS") +
  ggsci::scale_fill_locuszoom()

ggsave('overlap.pdf', p)

```