---
title: "12-DEG_venn"
output: html_document
date: "2025-03-21"
---
### Load libraries
```{r}
library(dplyr)
library(ggplot2)
if (!require(devtools)) install.packages("devtools")
devtools::install_github("yanlinlin82/ggvenn")
library(ggvenn)
```

### Load DEGS
```{r}
# Gill (TC)
GOW_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/GOW_sigs_merged.csv")
GOA_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/GOA_sigs_merged.csv")
GDO_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/GDO_sigs_merged.csv")

# Foot (TC)
FOW_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/FOW_sigs_merged.csv")
FOA_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/FOA_sigs_merged.csv")
FDO_sigs <- read_table("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/DEG_lists/GOterms_genome/FDO_sigs_merged.csv")

# Select only unique identifiers
GOW_sigs <- unique(GOW_sigs)
GOA_sigs <- unique(GOA_sigs)
GDO_sigs <- unique(GDO_sigs)

FOW_sigs <- unique(FOW_sigs)
FOA_sigs <- unique(FOA_sigs)
FDO_sigs <- unique(FDO_sigs)


```

### Make lists for venn diagram
```{r}
G_list <- list(
  "Ocean warming" = GOW_sigs$`"gene"`, 
  "Ocean acidification" = GOA_sigs$`"gene"`, 
  "Hypoxia" = GDO_sigs$`"gene"`
  )

F_list <- list(
  "Ocean warming" = FOW_sigs$`"gene"`, 
  "Ocean acidification" = FOA_sigs$`"gene"`, 
  "Hypoxia" = FDO_sigs$`"gene"`
)
```

### Gill tissue venn diagram all treatments
```{r}
ggvenn(
  G_list, 
  fill_color = c("orange", "red", "green"),
  stroke_size = 0.5, set_name_size = 7
  )+
  theme(aspect.ratio = 1)
```
### Foot tissue venn all treatments
```{r}
ggvenn(
  F_list, 
  fill_color = c("orange", "red", "green"),
  stroke_size = 0.5, set_name_size = 7
  )+
  theme(aspect.ratio = 1)
```
### Make lists for tissue comparison within treatments
```{r}
DO_list <- list(
  Foot = FDO_sigs$`"gene"`,
  Gill = GDO_sigs$`"gene"`
)

OW_list <- list(
  Foot = FOW_sigs$`"gene"`,
  Gill = GOW_sigs$`"gene"`
)

OA_list <- list(
  Foot = FOA_sigs$`"gene"`,
  Gill = GOA_sigs$`"gene"`
)
```

### DO
```{r}

ggvenn(
  DO_list, 
  fill_color = c("pink", "purple"),
  stroke_size = 0.5, set_name_size = 7
  )
```
## OA
```{r}

ggvenn(
  OA_list, 
  fill_color = c("pink", "purple"),
  stroke_size = 0.5, set_name_size = 7
  )
```
## OW
```{r}

ggvenn(
  OW_list, 
  fill_color = c("pink", "purple"),
  stroke_size = 0.5, set_name_size = 7
  )
```