# PhyloTree

> PhyloTree reads a tree in Newick format (Newick::parse, which says where a malformed string goes wrong) and grows it from the root at the left, width…

Page: https://fframes-kit.pages.dev/docs/biology/phylo-tree/
Cargo feature: `biology` (`fframes-kit = { version = "..", features = ["biology"] }`)

`PhyloTree` reads a tree in Newick format (`Newick::parse`, which says where a malformed
string goes wrong) and grows it from the root at the left, `width` pixels from the root to
the leaves and `row` pixels between leaves:

- **Scale:** when every branch has a length the tree is drawn to scale; otherwise it is a
  cladogram, with the leaves in one column.
- **Growth:** from `delay` the branches draw outward one level every `step` seconds, and each
  leaf's name appears as its branch arrives.
- **Traits:** named inner nodes are traits shared by everything after them, marked on the
  branch that leads to them (`(Mouse,Human)hair`).
- **Highlight:** `highlight` names a node whose clade turns `highlight_color` at
  `highlight_at`.

Names with spaces are quoted (`'four limbs'`) or written with `_`. Gallery scene:
`PhyloTree` (vertebrates, then the mammals).

Gallery clip of `PhyloTree`: https://fframes-kit.pages.dev/media/scenes/PhyloTree-805f494b.mp4

```rust
use fframes_kit::prelude::*;
use fframes_kit::kits::biology::Newick;

let tree = Newick::parse("((Cat:1,Dog:1):2,Fish:3)root;").unwrap();
assert_eq!(tree.leaves(), ["Cat", "Dog", "Fish"]);
assert!(Newick::parse("((Cat,Dog)").is_err());

fn pets<'a>(ui: &mut Ui<'a, '_, '_>) -> Svgr<'a> {
    ui.show(PhyloTree {
        newick: "((Cat:1,Dog:1)mammals:2,Fish:3);".into(),
        highlight: Some("mammals".into()),
        highlight_at: 3.0,
        ..ui.defaults()
    })
}
```

## API

Components are plain structs. Set the fields you need and fill the rest with `..ui.defaults()`: the defaults below come from the current theme (`theme.` values are fields of `Theme`).

### PhyloTree

| Field | Type | Default | Description |
| --- | --- | --- | --- |
| `newick` | `String` | — | The tree in Newick notation, e.g. `((a:1,b:1)c:2,d:3);`; branch lengths are optional. |
| `delay` | `f32` | `0.0` | Seconds after the container's start before the first branches draw. |
| `step` | `f32` | `0.55` | Seconds each level of branches takes to draw outward. |
| `center` | `(f64, f64)` | `(-0.7, -0.4)` | The middle of the tree, in units of `ui.space`. |
| `width` | `f32` | `1000.0` | Pixels from the root to the leaves. |
| `row` | `f32` | `66.0` | Pixels between neighbouring leaves. |
| `highlight` | `Option<String>` | `None` | Name of a node whose clade is highlighted; `None` for none. |
| `highlight_at` | `f32` | `0.0` | Seconds after `delay` when the highlighted clade starts to turn `highlight_color`. |
| `branch_color` | `Color` | `theme.colors.muted` | Colour of the branches. |
| `highlight_color` | `Color` | `theme.colors.accent` | Colour the highlighted clade turns. |
| `trait_color` | `Color` | `Color::hex("#ffd43b")` | Colour of the trait marks and names on the branches. |
| `name_style` | `TextStyle` | `theme.typography.caption` | The font of the leaf names: family, size in pixels and weight. |
| `trait_style` | `TextStyle` | `trait_style` | The font of the trait names: family, size in pixels and weight. |
| `text_color` | `Color` | `theme.colors.text` | Colour of the leaf names. |
| `enter` | `Option<FadeIn>` | `None` | Fade in at the start; `None` for none. |
| `exit` | `Option<FadeOut>` | `None` | Fade out before the end; `None` for none. |

Feature `biology` · [Source](https://github.com/khanhthanhdev/fframes-kit/blob/main/fframes-kit/src/kits/biology/phylo.rs#L265)