rectree2svg
Build a svg representation of a phylogenetic reconciled (or not) tree
Keywords: phylogeny, reconciled trees, phylogenetic trees
Read a recphyloxml file: create a svg representation of the gene trees and species tree with events (loss, duplication, speciation, transfer).
Read a newick or phyloxml file: create a svg representation of the tree.
You may use the rectree2svg binary as well as the rust rectree2svg funtions to manipulate or draw phylogenetic trees (see "Using the code")
Currently under development.
Output example
Under development:
- Possible problem with the obsolete version of recPhyloXML format (speciationLoss is supported, speciationOutLoss and speciationOut are not supported yet)
- Allow 2/3 reconciliation levels (host/species/gene)
Instructions:
- cargo build --release
- target/release/rectree2svg -h
Help:
Read a newick, phyloxml or recPhyloXML file and create a svg.
Format is guessed according to filename (default is newick)
Usage:
target/release/rectree2svg -f input file [-b][-h][-i][-I][-l factor][-o output file][-p][-r ratio][-s][-v]
-b : open svg in browser
-h : help
-i : display internal gene nodes
-I : display internal species nodes
-l factor: use branch length, using the given factor
-o outputfile : set name of output file
-p : build a phylogram
-r ratio : set the ratio between width of species and gene tree.
Default 1.0, you usualy do not need to change it.
-s : drawing species tree only
-v : verbose
Input format is guessed according to the file name extension:
- .xml => phyloxml
- .phyloxml => phyloXML
- .recphyloxml => recPhyloXML
- .recPhyloXML => recPhyloXML
- .recphylo => recPhyloXML
- any other => newick
Using the code
https://crates.io/crates/rectree2svg
Simple Rust example: read a newick.txt file and creates the svg
use rectree2svg::{ArenaTree,Options,newick2tree,knuth_layout,check_contour_postorder,
shift_mod_xy,set_middle_postorder,draw_tree};
use std::fs;
fn main() {
let mut tree: ArenaTree<String> = ArenaTree::default();
let options: Options = Options::new();
let contents = fs::read_to_string("newick.txt")
.expect("Something went wrong reading the newick file");
let root = tree.new_node("Root".to_string());
newick2tree(contents, &mut tree, root, &mut 0);
knuth_layout(&mut tree,root, &mut 1);
check_contour_postorder(&mut tree, root);
shift_mod_xy(&mut tree, root, &mut 0.0, &mut 0.0);
set_middle_postorder(&mut tree, root);
draw_tree(&mut tree,"my_svg.svg".to_string(),&options);
}
Some newick examples are available here : https://github.com/simonpenel/rectree2svg/tree/master/newick_examples
Simple Rust example: build a gene tree with a duplication and creates the svg
use rectree2svg::{ArenaTree,Options,Event,knuth_layout,check_contour_postorder,
cladogramme,shift_mod_xy,set_middle_postorder,draw_tree};
fn main() {
let mut tree: ArenaTree<String> = ArenaTree::default();
let mut options: Options = Options::new();
// Create a new node root
let root = tree.new_node("root".to_string());
// Create new nodes
let a1 = tree.new_node("a1".to_string());
let a2 = tree.new_node("a2".to_string());
let a = tree.new_node("a".to_string());
let b = tree.new_node("b".to_string());
let c = tree.new_node("c".to_string());
let d = tree.new_node("d".to_string());
// Set names
tree.arena[root].name = "MyRoot".to_string();
tree.arena[a].name = "Gene A".to_string();
tree.arena[a1].name = "Gene A1".to_string();
tree.arena[a2].name = "Gene A2".to_string();
tree.arena[b].name = "Gene B".to_string();
tree.arena[c].name = "Gene C".to_string();
tree.arena[d].name = "Gene D".to_string();
// Set hierarchy
// a1 and a2 are children of a
tree.arena[a1].parent = Some(a);
tree.arena[a2].parent = Some(a);
tree.arena[a].children.push(a1);
tree.arena[a].children.push(a2);
// a and b are children of c
tree.arena[a].parent = Some(c);
tree.arena[b].parent = Some(c);
tree.arena[c].children.push(a);
tree.arena[c].children.push(b);
// c and d are children of root
tree.arena[c].parent = Some(root);
tree.arena[d].parent = Some(root);
tree.arena[root].children.push(c);
tree.arena[root].children.push(d);
// set duplication
tree.arena[a].e = Event::Duplication;
knuth_layout(&mut tree,root, &mut 1);
// Display cladogram
cladogramme(&mut tree);
check_contour_postorder(&mut tree, root);
shift_mod_xy(&mut tree, root, &mut 0.0, &mut 0.0);
set_middle_postorder(&mut tree, root);
// Display internal nodes
options.gene_internal = true ;
draw_tree(&mut tree,"my_svg.svg".to_string(),&options);
}
Code Examples
You may try the codes in the 'examples' directory:
cargo run --example read_newick
cargo run --example build_tree
cargo run --example lca
cargo run --example modify_tree
Source documentation
See Rust documentation : https://docs.rs/rectree2svg/
RecPhyloXML documentation
See http://phylariane.univ-lyon1.fr/recphyloxml/
Tree drawing algorithms and structures
"Arena" Tree structure is inspired by the code proposed here