240723_GO_network.Rmd

---
ttitle: "GO over SN and LC genes"
author: "Camila Arcuschin; Ignacio Schor"
date: "`r Sys.Date()`"
output: 
  html_document:
    toc: true
    theme: cerulean
    code_folding: hide
    out.width: 6
    out.heigh: 6
    fig.width: 6
    fig.height: 6
editor_options: 
  markdown: 
  wrap: 72
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(message = FALSE, echo = TRUE, warning = FALSE, dpi = 500) #dev = c('pdf', 'png') # If I want to export plots but don't look to the html (because it is too heavy). Remember to also add: clean = FALSE, as a parameter of the rmarkdown::render() function, when executing 
knitr::opts_knit$set(root.dir = "/data_husihuilke/shared/SMB/carcu/Parkinsons_project/")
```

```{r}
library(tidyverse)
library(org.Mm.eg.db)
library(clusterProfiler)
# library(ReactomePA)
library(enrichplot)
# library(biomaRt)
# library(DOSE)
# library(AnnotationHub)
```


```{r}
# Plot all terms from differentially enriched
enrichPlot <- function(x, n, title = NULL, cutoff) {
  p <- x %>% 
    mutate(OddsRatio = (as.numeric(sub("/.*", "", x$GeneRatio)) / as.numeric(sub(".*/", "", x$GeneRatio))) / 
             (as.numeric(sub("/.*", "", x$BgRatio)) / as.numeric(sub(".*/", "", x$BgRatio))),
           FDR = p.adjust,
           Description = factor(Description, levels = Description[order(-log10(FDR))])) %>% 
    filter(FDR <= cutoff)
  p <-head(p, n) %>% 
    ggplot() +
    geom_point(aes(x = -log10(FDR), y = Description,
                   color = -log10(FDR), size = Count)) +
    labs(x = "-log10(FDR)", y = "", color = expression(-log[10]~"adjusted p-value"), size = "gene count", title = title) +
    theme_linedraw() +
    theme(panel.grid = element_blank()) +
    scale_color_continuous(high = "#132B43", low = "#56B1F7")
  return(p)
}

date = 240723

regulon_SN_terms <- read_csv("Outputs/GRNdb_mouse_sc_whole_Brain-regulons_hyperrestricted_allupdown_hyperrstricted_session_edited_updown_regulators.csv")
regulon_selected <- filter(regulon_SN_terms, selected == T)

Uni <- regulon_SN_terms$`shared name` %>% unique()

regulon_selected_notDE <- filter(regulon_selected, (gene_class_allupdown == "none" | is.na(gene_class_allupdown)))

Enrich1stDS_Clusti_up <- enrichGO(regulon_selected_notDE$`shared name`,  pvalueCutoff = 1, OrgDb = "org.Mm.eg.db", keyType = "SYMBOL", ont = "BP", minGSSize = 5, universe = Uni) 
if (!(is.null(Enrich1stDS_Clusti_up))) {
  if (nrow(Enrich1stDS_Clusti_up@result) > 0){
  write_csv(Enrich1stDS_Clusti_up@result, paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators.csv"))
  enrichPlot(Enrich1stDS_Clusti_up@result, 20, paste0("GO: SN updown regulators "), cutoff = 0.05)
  ggsave(paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators.png"), width = 15, height = 10)
  }
}

Enrich1stDS_Clusti_up <- enrichGO(regulon_selected$`shared name`,  pvalueCutoff = 1, OrgDb = "org.Mm.eg.db", keyType = "SYMBOL", ont = "BP", minGSSize = 5, universe = Uni) 
if (!(is.null(Enrich1stDS_Clusti_up))) {
  if (nrow(Enrich1stDS_Clusti_up@result) > 0){
  write_csv(Enrich1stDS_Clusti_up@result, paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators_and_targets.csv"))
  enrichPlot(Enrich1stDS_Clusti_up@result, 20, paste0("GO: SN updown regulators and targets"), cutoff = 0.05)
  ggsave(paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators_and_targets.png"), width = 15, height = 10)
  }
}

Mouse_sc_whole_brain <- read_tsv("Data/Networks/GRNdb_mouse_sc_whole_Brain-regulons.txt")
Uni <- c(Mouse_sc_whole_brain$TF, Mouse_sc_whole_brain$gene) %>%  unique()

Enrich1stDS_Clusti_up <- enrichGO(regulon_selected$`shared name`,  pvalueCutoff = 1, OrgDb = "org.Mm.eg.db", keyType = "SYMBOL", ont = "BP", minGSSize = 5, universe = Uni) 
if (!(is.null(Enrich1stDS_Clusti_up))) {
  if (nrow(Enrich1stDS_Clusti_up@result) > 0){
  write_csv(Enrich1stDS_Clusti_up@result, paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators_and_targets_UniwholeGRN.csv"))
  enrichPlot(Enrich1stDS_Clusti_up@result, 20, paste0("GO: SN updown regulators and targets Uni whole GRN"), cutoff = 0.05)
  ggsave(paste0("Outputs/", date, "_GO_ORA_SN_updown_regulators_and_targets_UniwholeGRN.png"), width = 15, height = 10)
  }
}


```