---
title: "Icteridae Data Vis"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
library(knitr)
library(flexdashboard)
library(tidyverse)
library(plotly)

# Measurement data: 

birds <- read.csv("birds_combined_v2.csv") 
birds <- as.tibble(birds) 

birds4 <- birds %>% 
  mutate(bill_W_to_D = bill_width/bill_depth, rel_tail = tail/length, rel_wing = wing_length/length, rel_tarsus = tarsus/length)

icteridae <- birds4 %>%
  filter(Family == "Icteridae")


# Data for tree: 
library(ape)
library(phytools)
library(phylocanvas)
library(phylobase)

emberizoid_phy <- read.nexus("~/Desktop/sptree_MCC.tre")

icteridae_phy <- extract.clade(emberizoid_phy, 1071)

```

Column 
-------------------------------------
    
### Tree: Icteridae
    
```{r}

write.tree(icteridae_phy, "icteridae_newick.tre")

icteridfile <- "~/Desktop/icteridae_newick.tre"
tree <- load.tree(icteridfile)

icterus_mrca <- names(phylobase::MRCA(tree, c("Icterus_pustulatus", "Icterus_maculialatus")))
north_mrca <- names(phylobase::MRCA(tree, c("Nesopsar_nigerrimus", "Molothrus_ater")))
south_mrca <- names(phylobase::MRCA(tree, c("Amblycercus_holosericeus", "Psarocolius_cassini")))

phycanv <- phylocanvas(tree, width = 400)
icterus_names <- get.descendants(tree, icterus_mrca)
north_names <- get.descendants(tree, north_mrca)
south_names <- get.descendants(tree, south_mrca)

for (nodename in icterus_names) {
  phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="red")
}
for (nodename in north_names) {
  phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="lightgreen")
}
for (nodename in south_names) {
  phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="blue")
}

phycanv

```
   
Column {.tabset}
-------------------------------------
   
### Body size by bill D/W

```{r}
p1 <- ggplot(icteridae, aes(x = log(length), y = bill_W_to_D)) + 
  geom_point(aes(group = Genus_species, colour = clade), alpha = 0.5, size = 4) + 
  labs(title = "Bill width to depth ratio and body length in North American blackbirds", y = "W/D") + 
  theme(legend.position="bottom", legend.box = "vertical")

ggplotly(p1, width = 500, height = 500, tooltip = c("group", "colour"))
```   
 
### Body size by relative tail length
    
```{r}
p2 <- ggplot(icteridae, aes(x = log(length), y = rel_tail)) + 
  geom_point(aes(group = Genus_species, colour = clade), alpha = 0.5, size = 4) + 
  labs(title = "Tail/body ratio and body length in North American blackbirds", y = "W/D") + 
  theme(legend.position="bottom", legend.box = "vertical")

ggplotly(p2, width = 500, height = 500, tooltip = c("group", "colour"))
```