FigS7.Rmd

---
title: "Fo lycopersici supercontig 51"
author: "Lily Peck"
date: "2024-09-20"
output: html_document
---

```{r setup, include=FALSE}
library(ggtree)
library(tidyverse)
library(treeio)
```


```{r species tree}
species.tree <- read.tree("./Data/Species_tree.treefile")

groups<-read.csv("/Users/lilypeck/Library/CloudStorage/OneDrive-ImperialCollegeLondon/Genomics/7_flye.LR/densitree/species.tree.tip.labelgroup", sep="\t",header = 1)

pal <- c("#74A089", "#F5CDB4", "#F8AFA8", "#9C964A", "#F98400","#FDDDA0")

g <- species.tree %>%
  ggtree(color="#000000") %<+% groups +
  geom_tiplab(aes(label=paste0('italic(', genus, ')~italic(', species, ')~', strain)), parse=T, size = 4, offset = .02, align = T) +
  geom_nodelab(hjust = 1.5, size = 3) +
  geom_tippoint(aes(x = x+.02, color=group),size=5, na.rm = TRUE) +
  scale_color_manual(values = pal,
                     #labels = c("Absent", "Intact"),
                     breaks = c("Robusta", "Coffea1","Coffea2","Arabica","FOSC","FFC"),
                                name = "") +
  theme(legend.position = "bottom",
        legend.text = element_text(size = 15),
        panel.background = element_rect(fill='transparent'), #transparent panel bg
        plot.background = element_rect(fill='transparent', color=NA)) +
  geom_treescale(offset = -1) +
  xlim(0,1)
g
```

```{r heatmap}
hits<-read.csv("./Data/Rob254.s709.genes_all.cds.blast.csv", sep=",",header = F)
hits <- hits[c(2:nrow(hits)),]
colnames(hits) <- hits[1,]
hits <- hits[2:nrow(hits),]
rownames(hits)<-hits$Gene
hits <- hits %>% 
  dplyr::select(!new.label) %>% 
  dplyr::select(!Gene) 

gheatmap(g,hits, offset = 0.3, width=2,
         colnames_position="bottom", 
         colnames_angle=-45, colnames_offset_y = -1.5, colnames_offset_x = .04,
         hjust=.5, font.size=3) +
  scale_fill_viridis_d(option = "inferno", direction = -1,
                       labels = c("Absent","Present")) +
  theme(legend.position = "bottom",
        legend.title = element_blank()) +
  scale_y_continuous(expand=c(0, 3))
ggsave("FigS7.tiff")
```