---
title: "12-Volcano_plots"
output: html_document
date: "2025-03-21"
---

### Load libraries
```{r}
library(dplyr)
library(ggplot2)
library(gridExtra)
```


### 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)


```


```{r}
my_theme <- theme_classic()+
    theme(axis.text.x = element_text(color="black",angle = 0, hjust = 0.5, size = 18),
        axis.title.x = element_text(color="black",size = 20),
        axis.title.y = element_text(color="black",size = 20),      
        axis.text.y = element_text(color="black",size = 18),
       legend.text = element_text(color="black",size = 18),      # Change legend text size
    legend.title = element_text(color="black",size = 20),
    legend.position = "none",
    panel.border = element_rect(colour = "black", fill=NA, linewidth=1))+
  theme(aspect.ratio = 1)
```

```{r}
FDO_volcano <- ggplot(FDO_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change") , 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
  my_theme +
  xlim(-6,6)+
  ylim(1,20)
    

FDO_volcano
```
```{r}
GDO_volcano <- ggplot(GDO_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change") , 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
  my_theme +
  xlim(-6,6)+
  ylim(1,20)
  
GDO_volcano

```
```{r}
FOW_volcano <- ggplot(FOW_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change") , 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
  my_theme +
  xlim(-6,6)+
  ylim(1,20)  

FOW_volcano
```
```{r}
GOW_volcano <- ggplot(GOW_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change"), 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
  my_theme+
  xlim(-6,6)+
  ylim(1,20)  

GOW_volcano 
```
```{r}

FOA_volcano <- ggplot(FOA_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change") , 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
  my_theme +
  xlim(-6,6)+
  ylim(1,20) 

FOA_volcano

```
```{r}
GOA_volcano <- ggplot(GOA_sigs, aes(x=`"log2FoldChange"`, y=-log10(`"padj"`))) +
    geom_point(aes(color= `"log2FoldChange"` > 0 )) +
    scale_color_manual(values=c("red", "blue")) +
    labs(x=expression(Log["2"]*" fold change") , 
         y=NULL) +
    theme(plot.title = element_text(hjust = 0.5))+
    my_theme+ 
  xlim(-6,6)+
  ylim(1,20)  

GOA_volcano
```
```{r}
grid.arrange(GOA_volcano, GOW_volcano, GDO_volcano,nrow = 1)
```
```{r}
grid.arrange(FOA_volcano, FOW_volcano, FDO_volcano,nrow = 1)
```