plot_pca.Rmd

---
title: "PCA plot"
author: "Gabriel Luis Hernandez"
output:
  pdf_document: default
  html_document: default
---
```{r echo=FALSE, message=FALSE, warning=FALSE}
libraries <- c("ggplot2", "gdsfmt", "SNPRelate", "MASS", "tidyverse", "ggtext", "ggrepel")
for (lib in libraries) {
  if (require(package = lib, character.only = TRUE)) {
    print("Successful")
  } else {
    print("Installing")
    if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
    }
    BiocManager::install(lib)
    library(lib, character.only = TRUE)
  }
}
```

```{r echo=FALSE, message=FALSE, warning=FALSE}
updated_tab <- read.csv("input/outgroup_edited.csv", header = TRUE, fill = TRUE)

Xlabs <- paste("PC2 ", PCA2, "%", sep = "")
Ylabs <- paste("PC1 ", PCA1, "%", sep = "")
```

# pca plot
```{r echo=FALSE, warning=FALSE}
pca_plot <- ggplot(data = updated_tab %>% arrange(desc(pop)), aes(x = EV2, y = EV1, )) +
  geom_point(aes(color = pop, stroke = 0.9, shape = super),
    alpha = 0.6, size = 2
  ) +
  guides(fill = FALSE, alpha = FALSE, size = FALSE) +
  labs(shape = "Supergene variant", color = "Species", x = Xlabs, y = Ylabs)

pca_plot_print <- pca_plot + scale_shape_manual(values = c(21, 24, 3, 22)) +
  scale_colour_manual(
    values = c(
      "#000000", "#ff0600", "#d87904", "#891bce",
      "#f71ae6", "#2bc100"
    ),
    labels = c(
      "S. 'AdRX'", "*S. interrupta*", "*S. invicta*",
      "*S. macdonaghi*", "*S. megergates*", "*S. richteri*"
    )
  ) +
  theme(legend.text = element_markdown(size = 8), legend.title = element_text(size = 9))

pca_plot_print
```

# pca with labels
```{r echo=FALSE, warning=FALSE}
pc12_plot <- ggplot(data = updated_tab %>% arrange(desc(pop)), aes(x = EV2, y = EV1, )) +
  geom_point(aes(color = pop, stroke = 0.9, shape = super),
    alpha = 0.6, size = 2
  ) +
  guides(fill = FALSE, alpha = FALSE, size = FALSE) +
  labs(shape = "Supergene variant", color = "Species", x = Xlabs, y = Ylabs)

pc12_plot_print <- pc12_plot + scale_shape_manual(values = c(21, 24, 3, 22)) +
  scale_colour_manual(values = c(
    "#000000", "#ff0600", "#d87904", "#891bce",
    "#f71ae6", "#2bc100"
  ), labels = c(
    "S. 'AdRX'",
    "*S. interrupta*", "*S. invicta*", "*S. macdonaghi*",
    "*S. megergates*", "*S. richteri*"
  )) +
  theme(legend.text = element_markdown(size = 8), legend.title = element_text(size = 9)) +
  geom_text(aes(label = ifelse(EV9 == 1, as.character(sample.id), ""), colour = pop),
    hjust = 1.1, vjust = 0, size = 2, check_overlap = FALSE, angle = 0
  ) +
  geom_text(aes(label = ifelse(EV9 == 2, as.character(sample.id), ""), colour = pop),
    hjust = -0.1, vjust = 0.9, size = 2, check_overlap = FALSE, angle = -14
  )

pc12_plot_print

dev.off()
```