enrichment-plot.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}
my_data <- read_csv('input/enrichment (13).csv') %>%
  janitor::clean_names()


my_data %>% 
  ggplot(aes(y = reorder(pathway, n_genes), x = 1)) +
  geom_point(aes(size = n_genes, color = enrichment_fdr)) +
  scale_y_discrete(position = "right") +
  theme(axis.title.x = element_blank(), 
        axis.text.x = element_blank(), 
        axis.ticks.x = element_blank(),
        panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank()) +
  labs(y = NULL, color = 'FDR', size = 'Genes')
```

```{r}
# 13.02.2022
my_data <- read_csv('input/enrichment (13).csv') %>%
  janitor::clean_names() %>% 
  mutate(term_id = str_replace(url, '.*/','')) 

my_revigo_data <-
  read_csv('input/RevigoTreeMap.csv', comment = '%') %>%
  janitor::clean_names() %>%
  mutate(name = str_replace_all(name,'"',''), name = str_to_lower(name))


my_data %>% 
  filter(term_id %in% my_revigo_data$term_id) %>%
  mutate(term_id = factor(term_id, levels = my_revigo_data$term_id)) %>%
  ggplot(aes(y = reorder(pathway, as.integer(term_id)), x = 1)) +
  geom_point(aes(size = n_genes, color = enrichment_fdr)) +
  scale_y_discrete(position = "right") +
  theme(axis.title.x = element_blank(), 
        axis.text.x = element_blank(), 
        axis.ticks.x = element_blank(),
        panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank()) +
  labs(y = NULL, color = 'FDR', size = 'Genes')
```