Phylustrator
A small, composable plotter for evolutionary figures. Two domains share one grammar: ph.trees
plots phylogenetic trees and ph.genomes plots genomes, synteny and alignments. Start a figure,
add layers with +, and save it to SVG, PDF, or PNG.
Install
pip install git+https://github.com/AADavin/Phylustrator
SVG output needs nothing else; for PDF/PNG also install cairosvg (pip install cairosvg).
Trees
import phylustrator as ph
tree = ph.trees.loads("((((Human:6,Chimp:6)a:2,Gorilla:8)b:3,Orang:11)c:5,Gibbon:16)root;")
brain = {"Human": 1350, "Chimp": 400, "Gorilla": 500, "Orang": 400, "Gibbon": 100,
"a": 650, "b": 560, "c": 500, "root": 470}
(ph.trees.plot(tree)
+ ph.trees.color_branches(brain)
+ ph.trees.tip_labels()
+ ph.trees.colorbar("brain size (cc)")
+ ph.trees.time_axis("million years")).save("tree.png")
That is the whole idea: plot(tree) starts a figure and each + layer adds one decoration.
- Layouts —
rectangular(default),radial,unrooted. - Layers —
color_branches,color_history,tip_labels,node_labels,tip_track,branch_events,branch_spindles,node_halves,colorbar,legend,time_axis,time_marker,scale_bar,note,title,highlight_clade,highlight_lineage,node_intervals,branch_spindles,node_halves.legendandnotetake a corner;titleis centred over the panel.branch_spindlesmarks a branch with a lens that fades into the branch's own colour, andnode_halvesputs a two-colour disc on a node. An event given tobranch_eventscan carry aweight, so arcs and marks scale with the count they stand for. - Panels —
node_points, placed under a rectangular tree withph.below(tree, panel). The panel shares the tree's time axis, so a value measured at a node sits directly under that node.
Genomes
The same grammar, for genome maps. Plot a genome as a line or a ring, colour genes by family or strand, link two genomes with synteny ribbons, or set a copy-number heatmap / alignment beside a tree.
import phylustrator as ph
G = ph.genomes.read_gff("genome.gff") # {name: Genome}
genome = next(iter(G.values()))
(ph.genomes.plot(genome, layout="circular", coordinates="nucleotide")
+ ph.genomes.genes(by="strand")
+ ph.genomes.position_axis()).save("ring.png")
- Layouts —
linear,circular, andstack(one genome per row, for synteny). - Layers —
genes,synteny,highlight,position_axis. - Panels —
heatmap,alignment, placed next to a tree withph.beside(tree, panel).
ZOMBI2 I/O
ph.zombi reads the output of the ZOMBI2 genome-evolution
simulator into the data models above — kept in one clearly-separated layer so the core stays
format-agnostic:
import phylustrator as ph
G = ph.zombi.read_genomes("run/genomes") # {lineage: Genome}
M = ph.zombi.read_profiles("run") # family x genome copy-number Matrix
aln = ph.zombi.read_alignment("run", family=0) # Alignment keyed by genome
tree = ph.zombi.read_species_tree("run") # a Tree
Command line
phyl is a one-shot tree viewer — hand it a Newick file:
phyl tree.nwk # render to a temporary PDF and open it
phyl tree.nwk -o fig.svg # save instead (format from the extension: .svg / .pdf / .png)
phyl tree.nwk --radial --no-labels
Flags: --layout {rectangular,radial,unrooted} (or --radial / --unrooted), --no-labels,
--node-labels, --no-stem, --no-open. Colouring and everything else live in the Python API.
Dependencies
Only drawsvg (plus cairosvg for PDF/PNG). No ete3, no matplotlib.
License
MIT — see LICENSE.
1 maintainer
Metadata
1 maintainer
Release files for phylustrator 0.13.0
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