tlogo 0.1.2.dev0__tar.gz → 0.1.3.dev0__tar.gz

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tlogo
-Version: 0.1.2.dev0
+Version: 0.1.3.dev0
 Summary: Sequence logo generator for aligned FASTA files
 Author-email: Troy Sincomb <troysincomb@gmail.com>
 License: MIT
@@ -24,6 +24,7 @@ Requires-Dist: biopython>=1.80
 Requires-Dist: matplotlib>=3.5
 Requires-Dist: logomaker>=0.8
 Requires-Dist: pandas>=1.3
+Requires-Dist: patchworklib>=0.6
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0; extra == "dev"
 Requires-Dist: hypothesis>=6.0; extra == "dev"

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "matplotlib>=3.5",
     "logomaker>=0.8",
     "pandas>=1.3",
+    "patchworklib>=0.6",
 ]
 
 [project.optional-dependencies]

tlogo-0.1.3.dev0/src/tlogo/__init__.py

@@ -0,0 +1,23 @@
+"""tlogo — Sequence logo generator for aligned FASTA files."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from tlogo.hxb2 import build_hxb2_map, build_reverse_hxb2_map
+from tlogo.io import parse_alignment
+from tlogo.logo import apply_nature_style, draw_logo
+from tlogo.matrix import build_logo_matrix
+
+try:
+    __version__ = version("tlogo")
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+__all__ = [
+    "__version__",
+    "apply_nature_style",
+    "build_hxb2_map",
+    "build_logo_matrix",
+    "build_reverse_hxb2_map",
+    "draw_logo",
+    "parse_alignment",
+]

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.2.dev0'
-__version_tuple__ = version_tuple = (0, 1, 2, 'dev0')
+__version__ = version = '0.1.3.dev0'
+__version_tuple__ = version_tuple = (0, 1, 3, 'dev0')
 
-__commit_id__ = commit_id = 'g8a81ed2c2'
+__commit_id__ = commit_id = 'g302e8747d'

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo/logo.py

@@ -60,6 +60,63 @@ def apply_nature_style() -> None:
     })
 
 
+def draw_logo(
+    ax: plt.Axes,
+    matrix: pd.DataFrame,
+    labels: list[str],
+    title: str = "",
+    color_scheme: str = "chemistry",
+    matrix_type: str = "information",
+) -> logomaker.Logo:
+    """Draw a sequence logo onto any matplotlib-compatible Axes.
+
+    This is the primary composable API for tlogo. It draws onto whatever
+    Axes it receives — including a ``patchworklib.Brick`` — without creating
+    a figure, calling ``tight_layout()``, saving, or closing. Those are the
+    caller's responsibility.
+
+    Args:
+        ax: Target matplotlib Axes (or patchworklib Brick).
+        matrix: Logomaker-compatible DataFrame (information, probability,
+            or counts).
+        labels: X-axis tick labels (e.g. HxB2 positions).
+        title: Panel title string.  Pass ``""`` for no title.
+        color_scheme: Amino acid color scheme name for logomaker.
+        matrix_type: One of ``"information"``, ``"probability"``, or
+            ``"counts"``.  Controls the y-axis label.
+
+    Returns:
+        The ``logomaker.Logo`` instance for further customization.
+    """
+    logo = logomaker.Logo(
+        matrix,
+        ax=ax,
+        color_scheme=color_scheme,
+        font_name="Arial",
+        stack_order="big_on_top",
+        vpad=0.04,
+        baseline_width=0.4,
+    )
+    logo.style_spines(spines=["top", "right"], visible=False)
+    logo.style_spines(spines=["left", "bottom"], visible=True)
+
+    n_positions = len(labels)
+    ax.set_xticks(range(n_positions))
+    ax.set_xticklabels(labels, rotation=90, fontsize=FONT_TICK_LABEL)
+    ax.set_ylabel(
+        _y_axis_label(matrix_type), fontsize=FONT_AXIS_LABEL, labelpad=4
+    )
+    if title:
+        ax.set_title(
+            title, fontsize=FONT_TITLE, fontweight="bold", pad=4, loc="left"
+        )
+    ax.yaxis.set_major_locator(
+        ticker.MaxNLocator(nbins=3, prune="both")
+    )
+
+    return logo
+
+
 def _y_axis_label(matrix_type: str) -> str:
     """Return y-axis label for the given matrix type.
 
@@ -120,7 +177,6 @@ def render_logo_plot(
     """
     apply_nature_style()
     output_path.parent.mkdir(parents=True, exist_ok=True)
-    y_label = _y_axis_label(matrix_type)
     n_positions = len(labels)
     fmt = output_path.suffix.lstrip(".") or "pdf"
 
@@ -136,27 +192,11 @@ def render_logo_plot(
         )
         fig, ax = plt.subplots(1, 1, figsize=(fig_width, PANEL_HEIGHT))
 
-        logo = logomaker.Logo(
-            matrix,
-            ax=ax,
+        draw_logo(
+            ax, matrix, labels,
+            title=f"{title} \u2014 {n_positions} selected positions",
             color_scheme=color_scheme,
-            font_name="Arial",
-            stack_order="big_on_top",
-            vpad=0.04,
-            baseline_width=0.4,
-        )
-        logo.style_spines(spines=["top", "right"], visible=False)
-        logo.style_spines(spines=["left", "bottom"], visible=True)
-
-        ax.set_xticks(range(n_positions))
-        ax.set_xticklabels(labels, rotation=90, fontsize=FONT_TICK_LABEL)
-        ax.set_ylabel(y_label, fontsize=FONT_AXIS_LABEL, labelpad=4)
-        ax.set_title(
-            f"{title} \u2014 {n_positions} selected positions",
-            fontsize=FONT_TITLE, fontweight="bold", pad=4, loc="left",
-        )
-        ax.yaxis.set_major_locator(
-            ticker.MaxNLocator(nbins=3, prune="both")
+            matrix_type=matrix_type,
         )
 
         plt.tight_layout(pad=0.4)
@@ -184,29 +224,11 @@ def render_logo_plot(
             sub_matrix = matrix.iloc[row_indices, :].copy()
             sub_matrix.index = range(len(row_indices))
 
-            logo = logomaker.Logo(
-                sub_matrix,
-                ax=ax,
+            draw_logo(
+                ax, sub_matrix, sub_labels,
+                title=f"{title} \u2014 {region_name}",
                 color_scheme=color_scheme,
-                font_name="Arial",
-                stack_order="big_on_top",
-                vpad=0.04,
-                baseline_width=0.4,
-            )
-            logo.style_spines(spines=["top", "right"], visible=False)
-            logo.style_spines(spines=["left", "bottom"], visible=True)
-
-            ax.set_xticks(range(len(row_indices)))
-            ax.set_xticklabels(
-                sub_labels, rotation=90, fontsize=FONT_TICK_LABEL
-            )
-            ax.set_ylabel(y_label, fontsize=FONT_AXIS_LABEL, labelpad=4)
-            ax.set_title(
-                f"{title} \u2014 {region_name}",
-                fontsize=FONT_TITLE, fontweight="bold", pad=4, loc="left",
-            )
-            ax.yaxis.set_major_locator(
-                ticker.MaxNLocator(nbins=3, prune="both")
+                matrix_type=matrix_type,
             )
 
         plt.tight_layout(pad=0.4, h_pad=0.6)

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo/window.py

@@ -5,21 +5,18 @@ from __future__ import annotations
 from pathlib import Path
 
 import matplotlib.pyplot as plt
-import matplotlib.ticker as ticker
 import logomaker
 
 from tlogo.constants import (
     FONT_ANIMAL_LABEL,
-    FONT_AXIS_LABEL,
     FONT_SUPTITLE,
-    FONT_TICK_LABEL,
     NATURE_DOUBLE_COL,
     NATURE_SINGLE_COL,
     PANEL_HEIGHT,
 )
 from tlogo.hxb2 import HxB2Position, build_reverse_hxb2_map, get_env_region
 from tlogo.io import sort_animal_groups
-from tlogo.logo import _save_figure, _y_axis_label, apply_nature_style
+from tlogo.logo import _save_figure, _y_axis_label, apply_nature_style, draw_logo
 from tlogo.matrix import find_variant_positions, resolve_window_cols
 
 
@@ -95,24 +92,15 @@ def render_window_logo(
         )
         matrix.index = range(len(matrix))
 
-        logo = logomaker.Logo(
-            matrix, ax=ax, color_scheme=color_scheme,
-            font_name="Arial", stack_order="big_on_top",
-            vpad=0.04, baseline_width=0.4,
-        )
-        logo.style_spines(spines=["top", "right"], visible=False)
-        logo.style_spines(spines=["left", "bottom"], visible=True)
-
-        ax.set_xticks(range(len(selected_cols)))
-        ax.set_xticklabels(labels, rotation=90, fontsize=FONT_TICK_LABEL)
-        ax.set_ylabel(y_label, fontsize=FONT_AXIS_LABEL, labelpad=4)
-        ax.set_title(
-            f"{animal_name}  (n={n_seqs})",
-            fontsize=FONT_ANIMAL_LABEL, loc="left",
-        )
-        ax.yaxis.set_major_locator(
-            ticker.MaxNLocator(nbins=3, prune="both")
+        draw_logo(
+            ax, matrix, labels,
+            title=f"{animal_name}  (n={n_seqs})",
+            color_scheme=color_scheme,
+            matrix_type=matrix_type,
         )
+        # Window mode uses a smaller title font than the standard logo
+        ax.title.set_fontsize(FONT_ANIMAL_LABEL)
+        ax.title.set_fontweight("normal")
 
     fig.tight_layout(rect=[0, 0, 1, 0.95])
     _save_figure(fig, output_path, fmt)

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tlogo
-Version: 0.1.2.dev0
+Version: 0.1.3.dev0
 Summary: Sequence logo generator for aligned FASTA files
 Author-email: Troy Sincomb <troysincomb@gmail.com>
 License: MIT
@@ -24,6 +24,7 @@ Requires-Dist: biopython>=1.80
 Requires-Dist: matplotlib>=3.5
 Requires-Dist: logomaker>=0.8
 Requires-Dist: pandas>=1.3
+Requires-Dist: patchworklib>=0.6
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0; extra == "dev"
 Requires-Dist: hypothesis>=6.0; extra == "dev"

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ src/tlogo.egg-info/requires.txt
 src/tlogo.egg-info/top_level.txt
 tests/conftest.py
 tests/test_cli.py
+tests/test_draw_logo.py
 tests/test_hxb2.py
 tests/test_io.py
 tests/test_matrix.py

{tlogo-0.1.2.dev0 → tlogo-0.1.3.dev0}/src/tlogo.egg-info/requires.txt

@@ -3,6 +3,7 @@ biopython>=1.80
 matplotlib>=3.5
 logomaker>=0.8
 pandas>=1.3
+patchworklib>=0.6
 
 [dev]
 pytest>=7.0

tlogo-0.1.3.dev0/tests/test_draw_logo.py

@@ -0,0 +1,143 @@
+"""Tests for the draw_logo() composable API."""
+
+from __future__ import annotations
+
+import matplotlib
+import matplotlib.pyplot as plt
+import logomaker
+import pytest
+
+from tlogo.logo import apply_nature_style, draw_logo
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _make_matrix() -> tuple:
+    """Build a small information matrix for testing."""
+    subsequences = ["ACDEF", "ACDEY", "ACDEW", "ACDEK", "ACDEF"]
+    matrix = logomaker.alignment_to_matrix(
+        subsequences,
+        to_type="information",
+        characters_to_ignore=".-",
+        pseudocount=1.0,
+    )
+    matrix.index = range(len(matrix))
+    labels = [str(i + 1) for i in range(len(matrix))]
+    return matrix, labels
+
+
+# ---------------------------------------------------------------------------
+# Tests
+# ---------------------------------------------------------------------------
+
+
+class TestDrawLogo:
+    """Tests for draw_logo on plain matplotlib Axes."""
+
+    def setup_method(self) -> None:
+        matplotlib.use("Agg")
+
+    def test_returns_logomaker_logo(self) -> None:
+        matrix, labels = _make_matrix()
+        _fig, ax = plt.subplots()
+        result = draw_logo(ax, matrix, labels)
+        assert isinstance(result, logomaker.Logo)
+        plt.close("all")
+
+    def test_sets_xtick_labels(self) -> None:
+        matrix, labels = _make_matrix()
+        _fig, ax = plt.subplots()
+        draw_logo(ax, matrix, labels)
+        tick_labels = [t.get_text() for t in ax.get_xticklabels()]
+        assert tick_labels == labels
+        plt.close("all")
+
+    def test_sets_title(self) -> None:
+        matrix, labels = _make_matrix()
+        _fig, ax = plt.subplots()
+        draw_logo(ax, matrix, labels, title="My Title")
+        # draw_logo sets title with loc="left"
+        assert ax.get_title(loc="left") == "My Title"
+        plt.close("all")
+
+    def test_empty_title_produces_no_title(self) -> None:
+        matrix, labels = _make_matrix()
+        _fig, ax = plt.subplots()
+        draw_logo(ax, matrix, labels, title="")
+        assert ax.get_title(loc="left") == ""
+        plt.close("all")
+
+    @pytest.mark.parametrize(
+        "matrix_type, expected_ylabel",
+        [
+            ("information", "Information (bits)"),
+            ("probability", "Frequency"),
+            ("counts", "Count"),
+        ],
+    )
+    def test_ylabel_matches_matrix_type(
+        self, matrix_type: str, expected_ylabel: str
+    ) -> None:
+        matrix, labels = _make_matrix()
+        _fig, ax = plt.subplots()
+        draw_logo(ax, matrix, labels, matrix_type=matrix_type)
+        assert ax.get_ylabel() == expected_ylabel
+        plt.close("all")
+
+    def test_does_not_create_or_close_figure(self) -> None:
+        """draw_logo must not call plt.close or create its own figure."""
+        fig, ax = plt.subplots()
+        matrix, labels = _make_matrix()
+        draw_logo(ax, matrix, labels)
+        # Figure should still be open
+        assert fig.number in plt.get_fignums()
+        plt.close("all")
+
+    def test_nature_style_applied(self) -> None:
+        apply_nature_style()
+        assert matplotlib.rcParams["axes.spines.top"] is False
+        assert matplotlib.rcParams["axes.spines.right"] is False
+
+
+# ---------------------------------------------------------------------------
+# Patchworklib integration (skip if not installed)
+# ---------------------------------------------------------------------------
+
+try:
+    import patchworklib as pw
+    _has_pw = True
+except ImportError:
+    _has_pw = False
+
+
+@pytest.mark.skipif(not _has_pw, reason="patchworklib not installed")
+class TestPatchworkIntegration:
+    """Verify draw_logo works with patchworklib Bricks."""
+
+    def setup_method(self) -> None:
+        matplotlib.use("Agg")
+
+    def test_draw_on_brick(self) -> None:
+        matrix, labels = _make_matrix()
+        brick = pw.Brick("test_logo", figsize=(4, 2))
+        result = draw_logo(brick, matrix, labels, title="Brick Logo")
+        assert isinstance(result, logomaker.Logo)
+        assert brick.get_title(loc="left") == "Brick Logo"
+
+    def test_compose_two_bricks(self, output_dir) -> None:
+        m1, l1 = _make_matrix()
+        m2, l2 = _make_matrix()
+
+        b1 = pw.Brick("logo_left", figsize=(4, 2))
+        b2 = pw.Brick("logo_right", figsize=(4, 2))
+
+        draw_logo(b1, m1, l1, title="Left")
+        draw_logo(b2, m2, l2, title="Right")
+
+        composed = b1 | b2
+        out = output_dir / "patchwork_composed.png"
+        composed.savefig(str(out))
+        assert out.exists()
+        assert out.stat().st_size > 0

tlogo-0.1.2.dev0/src/tlogo/__init__.py

@@ -1,8 +0,0 @@
-"""tlogo — Sequence logo generator for aligned FASTA files."""
-
-from importlib.metadata import PackageNotFoundError, version
-
-try:
-    __version__ = version("tlogo")
-except PackageNotFoundError:
-    __version__ = "0.0.0"