phylustrator 0.2.2__tar.gz → 0.2.3__tar.gz

{phylustrator-0.2.2/src/phylustrator.egg-info → phylustrator-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.2.2
+Version: 0.2.3
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.2.2 → phylustrator-0.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "phylustrator"
-version = "0.2.2"
+version = "0.2.3"
 description = "A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments"
 readme = "README.md"
 requires-python = ">=3.10"

{phylustrator-0.2.2 → phylustrator-0.2.3}/src/phylustrator/genomes/figure.py

@@ -25,7 +25,7 @@ _LAYOUTS = {"linear": linear, "circular": circular}
 
 class Figure:
     def __init__(self, genome, *, layout: str = "linear", coordinates: str = "ordered",
-                 style: Style | None = None, layers: tuple = ()) -> None:
+                 style: Style | None = None, layers: tuple = (), **layout_kw) -> None:
         if layout not in _LAYOUTS:
             raise ValueError(f"unknown layout {layout!r}; choose from {sorted(_LAYOUTS)}")
         self.genome = genome
@@ -33,13 +33,15 @@ class Figure:
         self.coordinates = coordinates
         self.style = style or Style()
         self.layers = tuple(layers)
+        self.layout_kw = dict(layout_kw)          # e.g. scale="shared" on a circular genome
 
     def _make_layout(self) -> Layout:
-        return _LAYOUTS[self.layout](self.genome, coordinates=self.coordinates, style=self.style)
+        return _LAYOUTS[self.layout](self.genome, coordinates=self.coordinates, style=self.style,
+                                     **self.layout_kw)
 
     def _clone(self, **kw) -> "Figure":
         base = dict(layout=self.layout, coordinates=self.coordinates, style=self.style,
-                    layers=self.layers)
+                    layers=self.layers, **self.layout_kw)
         base.update(kw)
         return Figure(self.genome, **base)  # type: ignore[arg-type]  # kw dict, params are typed
 
@@ -85,9 +87,11 @@ class StackFigure(Figure):
 
 
 def plot(genome, *, layout: str = "linear", coordinates: str = "ordered",
-         style: Style | None = None) -> Figure:
-    """Start a figure for one ``genome``. Add layers with ``+``, then :meth:`Figure.save`."""
-    return Figure(genome, layout=layout, coordinates=coordinates, style=style)
+         style: Style | None = None, **layout_kw) -> Figure:
+    """Start a figure for one ``genome``. Add layers with ``+``, then :meth:`Figure.save`.
+
+    Extra keywords reach the layout — ``scale="shared"`` on a circular genome, for one."""
+    return Figure(genome, layout=layout, coordinates=coordinates, style=style, **layout_kw)
 
 
 def stack(genomes, *, coordinates: str = "ordered", style: Style | None = None) -> StackFigure:

{phylustrator-0.2.2 → phylustrator-0.2.3}/src/phylustrator/genomes/layout.py

@@ -90,27 +90,40 @@ def stacked(genomes, *, coordinates: str = "ordered", gap: float = 0.16,
 
 
 def circular(genome, *, coordinates: str = "ordered", gap: float = 0.16,
-             start_deg: float = 90.0, break_deg: float = 0.0,
+             start_deg: float = 90.0, break_deg: float = 0.0, scale: str = "each",
              band: float = 0.34, ring_gap: float = 0.10, min_deg: float = 2.2, style=None) -> Layout:
     """Genes wrapped onto a ring, one concentric ring per chromosome (chromosome 0 outermost).
 
     Angles sweep **clockwise** from the top. By default the ring is closed (``break_deg=0``) so genes
     are evenly spaced all the way round; set ``break_deg`` to leave a wedge marking a linear
     chromosome's ends. ``coordinates`` chooses equal angular slots by **rank** (``"ordered"``) or
-    base-proportional arcs (``"nucleotide"``)."""
+    base-proportional arcs (``"nucleotide"``).
+
+    ``scale`` decides what a ring's angles mean when a genome has several chromosomes:
+
+    ``"each"`` (default) gives every chromosome the whole circle, so gene *order* is comparable ring
+    to ring and a chromosome's size is not. ``"shared"`` gives every gene the same angular width,
+    taken from the largest chromosome, so a short chromosome draws a short arc — which is what a
+    **karyotype** needs. Under ``"each"`` a three-gene chromosome is a full circle of three enormous
+    wedges beside a seventy-gene ring, and the picture says they are the same size."""
     start = math.radians(start_deg)
     sweep = 2.0 * math.pi - math.radians(break_deg)
     boxes, owner, placed, rings, totals = {}, {}, [], [], []
+    if scale not in ("each", "shared"):
+        raise ValueError(f"unknown scale {scale!r}; choose 'each' or 'shared'")
+    widest = max((len(c.genes) for c in genome.chromosomes), default=1) or 1
     for k, chrom in enumerate(genome.chromosomes):
         R = 1.0 - band / 2.0 - k * (band + ring_gap)
         rings.append(R)
         n = len(chrom.genes)
         nuc = coordinates == "nucleotide" and n and chrom.genes[0].start is not None
         total = float(chrom.length or (chrom.genes[-1].end - chrom.genes[0].start) or 1.0) if nuc \
-            else float(n or 1)
+            else float(widest if scale == "shared" else (n or 1))
         totals.append(total)
-        # cap the minimum arc so a gene-dense genome (a real GFF) never forces genes to overlap
-        min_arc = min(math.radians(min_deg), 0.9 * sweep / max(n, 1))
+        # cap the minimum arc so a gene-dense genome (a real GFF) never forces genes to overlap.
+        # The cap counts the ring's own slots: under "shared" that is the widest chromosome, so a
+        # short ring is never inflated back to the width it would have had on its own.
+        min_arc = min(math.radians(min_deg), 0.9 * sweep / max(n if nuc else total, 1.0))
         _ = style  # (thickness is read from style at draw time via ring_hh below)
         for rank, gene in enumerate(chrom.genes):        # rank, so "ordered" is even with no holes
             lo_v, hi_v = (float(gene.start), float(gene.end)) if nuc \

{phylustrator-0.2.2 → phylustrator-0.2.3/src/phylustrator.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.2.2
+Version: 0.2.3
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.2.2 → phylustrator-0.2.3}/tests/test_genomes.py

@@ -22,6 +22,7 @@ from phylustrator.genomes import (
     synteny,
     tracks,
 )
+from phylustrator.genomes.layout import circular
 from phylustrator.trees import loads
 from phylustrator.trees import plot as tree_plot
 
@@ -57,6 +58,22 @@ def test_position_axis_on_nucleotide_ring():
     assert svg.lstrip().startswith("<")
 
 
+def test_circular_shared_scale_shortens_the_small_chromosome():
+    """A karyotype: under ``scale="shared"`` a short chromosome draws a short arc."""
+    big = _genome("g", list("12345678")).chromosomes[0]
+    small = Chromosome(id="c2", genes=_genome("s", ["9", "10"]).chromosomes[0].genes,
+                       topology="circular", length=200)
+    g = Genome(name="k", chromosomes=[big, small])
+    arc = {}
+    for scale in ("each", "shared"):
+        lay = circular(g, scale=scale)
+        a0, a1, _ = lay.boxes[id(small.genes[0])]
+        arc[scale] = abs(a1 - a0)
+    assert arc["shared"] < arc["each"] / 3          # 8 slots wide, not 2
+    with pytest.raises(ValueError, match="unknown scale"):
+        circular(g, scale="both")
+
+
 def test_heatmap_panel_beside_tree():
     tree = tree_plot(loads("(a:1,b:1)R;"))
     m = Matrix(rows=["a", "b"], cols=["f1", "f2", "f3"], values=[[1, 0, 2], [0, 1, 1]])