marsilea 0.4.1__py3-none-any.whl → 0.4.3__py3-none-any.whl

marsilea/plotter/text.py

@@ -10,6 +10,7 @@ import warnings
 from dataclasses import dataclass
 from matplotlib.axes import Axes
 from matplotlib.colors import is_color_like
+from matplotlib.lines import Line2D
 from matplotlib.patches import Rectangle
 from matplotlib.text import Text
 from typing import List, Iterable
@@ -389,7 +390,7 @@ class _LabelBase(RenderPlan):
         ax.remove()
         return np.max(sizes) / figure.get_dpi()
 
-    def get_canvas_size(self, figure):
+    def get_canvas_size(self, figure, **kwargs):
         self.texts_size = self.silent_render(figure, expand=self.get_expand())
         return self.texts_size + self.padding / 72
 
@@ -545,7 +546,7 @@ class AnnoLabels(_LabelBase):
         p.update_params(self._user_params)
         return p
 
-    def get_canvas_size(self, figure):
+    def get_canvas_size(self, figure, **kwargs):
         expand = self.get_expand()
         canvas_size = self.silent_render(figure, expand)
         size = canvas_size + self.pointer_size
@@ -651,7 +652,7 @@ class Labels(_LabelBase):
         >>> import marsilea as ma
         >>> from marsilea.plotter import Labels
         >>> h = ma.Heatmap(np.random.randn(20, 20))
-        >>> h.add_right(Labels(labels, text_props={'color': colors}))
+        >>> h.add_right(Labels(labels, text_props={"color": colors}))
         >>> h.render()
 
     """
@@ -778,10 +779,10 @@ class Title(_LabelBase):
         >>> matrix = np.random.randn(15, 10)
         >>> h = ma.Heatmap(matrix)
         >>> for align in ["left", "right", "center"]:
-        ...     title = Title(f'Title align={align}', align=align)
+        ...     title = Title(f"Title align={align}", align=align)
         ...     h.add_top(title)
         >>> for align in ["top", "bottom", "center"]:
-        ...     title = Title(f'Title align={align}', align=align)
+        ...     title = Title(f"Title align={align}", align=align)
         ...     h.add_left(title)
         >>> h.render()
 
@@ -887,6 +888,7 @@ class _ChunkBase(_LabelBase):
         align=None,
         props=None,
         padding=2,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -910,6 +912,7 @@ class _ChunkBase(_LabelBase):
             props = [props for _ in range(n)]
         self.props = props
 
+        self.underline = underline
         if is_color_like(bordercolor):
             bordercolor = [bordercolor for _ in range(n)]
         if bordercolor is not None:
@@ -924,6 +927,12 @@ class _ChunkBase(_LabelBase):
             borderstyle = [borderstyle for _ in range(n)]
         self.borderstyle = borderstyle
 
+        if self.underline:
+            if self.bordercolor is None:
+                self.bordercolor = np.asarray(["black" for _ in range(n)])
+            if self.borderwidth is None:
+                self.borderwidth = np.asarray([3 for _ in range(n)])
+
         self._draw_bg = (self.fill_colors is not None) or (self.bordercolor is not None)
         self.text_pad = 0
 
@@ -941,6 +950,13 @@ class _ChunkBase(_LabelBase):
         "bottom": 0,
     }
 
+    default_underline = {
+        "right": [(0, 0), (0, 1)],
+        "left": [(1, 1), (1, 0)],
+        "top": [(0, 1), (0, 0)],
+        "bottom": [(0, 1), (1, 1)],
+    }
+
     def get_alignment(self, ha, va, rotation):
         if rotation in {90, -90}:
             ha, va = va, ha  # swap the alignment
@@ -1005,16 +1021,27 @@ class _ChunkBase(_LabelBase):
             if self._draw_bg:
                 if bgcolor is None:
                     bgcolor = "white"
-                rect = Rectangle(
-                    (0, 0),
-                    1,
-                    1,
-                    facecolor=bgcolor,
-                    edgecolor=bc,
-                    linewidth=lw,
-                    linestyle=ls,
-                    transform=ax.transAxes,
-                )
+                if not self.underline:
+                    rect = Rectangle(
+                        (0, 0),
+                        1,
+                        1,
+                        facecolor=bgcolor,
+                        edgecolor=bc,
+                        linewidth=lw,
+                        linestyle=ls,
+                        transform=ax.transAxes,
+                    )
+                else:
+                    xdata, ydata = self.default_underline[self.side]
+                    rect = Line2D(
+                        xdata,
+                        ydata,
+                        color=bc,
+                        linewidth=lw,
+                        linestyle=ls,
+                        transform=ax.transAxes,
+                    )
                 ax.add_artist(rect)
                 fontdict.setdefault("color", self.get_text_color(bgcolor))
 
@@ -1069,10 +1096,10 @@ class Chunk(_ChunkBase):
         >>> from marsilea.plotter import Chunk
         >>> matrix = np.random.randn(20, 20)
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2', 'C3', 'C4']
+        >>> chunk = ["C1", "C2", "C3", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(Chunk(chunk, bordercolor="gray"), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(Chunk(chunk, bordercolor="gray"), pad=0.1)
         >>> h.add_dendrogram("left")
         >>> h.render()
 
@@ -1086,6 +1113,7 @@ class Chunk(_ChunkBase):
         align=None,
         props=None,
         padding=8,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -1100,6 +1128,7 @@ class Chunk(_ChunkBase):
             align=align,
             props=props,
             padding=padding,
+            underline=underline,
             bordercolor=bordercolor,
             borderwidth=borderwidth,
             borderstyle=borderstyle,
@@ -1175,10 +1204,10 @@ class FixedChunk(_ChunkBase):
         >>> from marsilea.plotter import FixedChunk
         >>> matrix = np.random.randn(20, 20)
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2', 'C3', 'C4']
+        >>> chunk = ["C1", "C2", "C3", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=0.1)
         >>> h.add_dendrogram("left")
         >>> h.render()
 
@@ -1188,12 +1217,18 @@ class FixedChunk(_ChunkBase):
         :context: close-figs
 
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2-1', 'C2-2', 'C4']
+        >>> chunk = ["C1", "C2-1", "C2-2", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=.1)
-        >>> h.add_right(FixedChunk(['C1', 'C2', 'C3'], fill_colors="red",
-        ...                        ratio=[1, 2, 1], ), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=0.1)
+        >>> h.add_right(
+        ...     FixedChunk(
+        ...         ["C1", "C2", "C3"],
+        ...         fill_colors="red",
+        ...         ratio=[1, 2, 1],
+        ...     ),
+        ...     pad=0.1,
+        ... )
         >>> h.render()
 
 
@@ -1208,6 +1243,7 @@ class FixedChunk(_ChunkBase):
         ratio=None,
         props=None,
         padding=8,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -1219,12 +1255,13 @@ class FixedChunk(_ChunkBase):
         super().__init__(
             texts,
             fill_colors,
-            align,
-            props,
-            padding,
-            bordercolor,
-            borderwidth,
-            borderstyle,
+            align=align,
+            props=props,
+            padding=padding,
+            underline=underline,
+            bordercolor=bordercolor,
+            borderwidth=borderwidth,
+            borderstyle=borderstyle,
             **options,
         )
         if ratio is not None:

marsilea/utils.py

@@ -2,7 +2,6 @@ import matplotlib as mpl
 import numpy as np
 from itertools import tee, islice
 from matplotlib import colors as mcolors
-from matplotlib.colors import Colormap
 from uuid import uuid4
 
 ECHARTS16 = [
@@ -69,15 +68,13 @@ def relative_luminance(color):
 
 
 def get_colormap(cmap):
-    if isinstance(cmap, Colormap):
-        return cmap
     try:
-        return mpl.colormap.get(cmap)
+        return mpl.colormaps.get_cmap(cmap)
     except AttributeError:
         try:
-            return mpl.cm.get_cmap(cmap)
+            return mpl.colormaps.get(cmap)
         except AttributeError:
-            return mpl.cm.ColormapRegistry.get_cmap(cmap)
+            return mpl.cm.get_cmap(cmap)
 
 
 def get_canvas_size_by_data(

marsilea-0.4.3.dist-info/METADATA

@@ -0,0 +1,168 @@
+Metadata-Version: 2.3
+Name: marsilea
+Version: 0.4.3
+Dynamic: Summary
+Project-URL: Home, https://github.com/Marsilea-viz/marsilea
+Author: Zhihang Zheng
+Author-email: Mr-Milk <yzheng@cemm.at>
+License: The MIT License (MIT)
+        
+        Copyright (c) 2024 Mr-Milk
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in
+        all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+        THE SOFTWARE.
+License-File: LICENSE
+Classifier: Framework :: Matplotlib
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Requires-Dist: legendkit
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: platformdirs
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Provides-Extra: dev
+Requires-Dist: icecream; extra == 'dev'
+Requires-Dist: mpl-fontkit; extra == 'dev'
+Requires-Dist: numpydoc; extra == 'dev'
+Requires-Dist: pydata-sphinx-theme; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: python-hmr; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-learn; extra == 'dev'
+Requires-Dist: sphinx; extra == 'dev'
+Requires-Dist: sphinx-copybutton; extra == 'dev'
+Requires-Dist: sphinx-design; extra == 'dev'
+Requires-Dist: sphinx-gallery; extra == 'dev'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture align="center">
+    <source media="(prefers-color-scheme: dark)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg">
+    <source media="(prefers-color-scheme: light)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-blue.jpg">
+    <img alt="Shows a bar chart with benchmark results." src="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg" width="400">
+  </picture>
+</p>
+
+[![Documentation Status](https://img.shields.io/readthedocs/marsilea?color=57B77E&logo=readthedocs&logoColor=white&style=flat-square)](https://marsilea.readthedocs.io/en/stable)
+![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
+![PyPI - License](https://img.shields.io/pypi/l/marsilea?color=FFD43B&style=flat-square)
+
+# Marsilea: Declarative creation of composable visualization!
+
+---
+
+## Documentation
+
+You can read the documentation on Read the Docs.
+
+[Read Documentation](https://marsilea.readthedocs.io/)
+
+## Installation
+
+```shell
+pip install marsilea
+```
+
+## What is Composable Visualization?
+
+<p align="center">
+  <picture align="center">
+    <img alt="Shows a bar chart with benchmark results." src="https://github.com/Marsilea-viz/marsilea/raw/main/img/showcase.gif" width="300">
+  </picture>
+</p>
+
+When we do visualization, we often need to combine multiple plots to show different aspects of the data.
+For example, we may need to create a heatmap to show the expression of genes in different cells,
+and then create a bar chart to show the expression of genes in different cell types.
+A visualization contains multiple plots is called a composable visualization.
+In Marsilea, we employ a declarative approach for user to create composable visualization incrementally.
+
+## Examples
+
+<table>
+    <thead>
+        <tr>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_tiobe_index.html">
+                    Bar Chart With Image
+                </a>
+            </th>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_oil_well.html">
+                    Stacked Bar
+                </a>
+            </th>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_arc_diagram.html">
+                    Arc Diagram
+                </a>
+            </th>
+        </tr>
+    </thead>
+    <tbody>
+        <tr>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_tiobe_index_001_2_00x.png" height="300px">
+            </td>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oil_well_001_2_00x.png" height="300px">
+            </td>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_arc_diagram_001_2_00x.png" width="300px">
+            </td>
+        </tr>
+    </tbody>
+</table>
+
+<table>
+    <thead>
+        <tr>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_pbmc3k.html">
+                    Heatmap
+                </a>
+            </th>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_oncoprint.html">
+                    Oncoprint
+                </a>
+            </th>
+            <th>
+                <a href="https://marsilea.readthedocs.io/en/latest/examples/Gallery/plot_upset.html">
+                    Upsetplot
+                </a>
+            </th>
+        </tr>
+    </thead>
+    <tbody>
+        <tr>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_pbmc3k_001_2_00x.png" width="300px">
+            </td>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oncoprint_005_2_00x.png" width="300px">
+            </td>
+            <td>
+                <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_upset_001_2_00x.png" width="300px">
+            </td>
+        </tr>
+    </tbody>
+</table>

marsilea-0.4.3.dist-info/RECORD

@@ -0,0 +1,30 @@
+marsilea/__init__.py,sha256=JcEA1veLIQxh9VhgwDL3yqf0Xo093E0yw3JvhDa5eqc,541
+marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
+marsilea/_deform.py,sha256=QRz4OGXMsQzbiIkC3ASzZayMPhHhoFsEK38oBzSeQG8,14440
+marsilea/base.py,sha256=aj15043lJURGR83T3q8Y8UUpeVHHLsi8T9VLol6KB1I,47552
+marsilea/dataset.py,sha256=a0mXjPu9_tRGHofnnQaTryFpxftkfqldq_ZLXMSBf7A,4410
+marsilea/dendrogram.py,sha256=Ung43zseybZKzTEvH5P_ge3WGfsr7i7qsX7YEVDlC74,15590
+marsilea/exceptions.py,sha256=wN5ElUZxuaJKSnnwWdkNx6P-Oc16dzSuaRPbRKWIBEM,1046
+marsilea/heatmap.py,sha256=UhRcBFhx1JKrtndZPvQCDaiMt8Pb314PT1BtL-JndCY,4208
+marsilea/layers.py,sha256=puXLlGGpEqAzaTqadpgpsYmIDPH33WyyHIuysRSqFZQ,12163
+marsilea/layout.py,sha256=X8MGPlAbbr7dcZiqW4pI7sEb8U3jVaiS7t1DKOqMYLI,27758
+marsilea/upset.py,sha256=U1Rsmo1WpCAV9z3LBlE2L4T0nAW9ols8Z36fXzmXycw,30388
+marsilea/utils.py,sha256=y_KYs4ToiuKEsiBdmcIVtmxMXFpD4wKiJ0k7iBa11z8,2854
+marsilea/plotter/__init__.py,sha256=6O05ShbbXdRmvbpLiEOBEZ_oZJkAMVh3Rh9jBU8QF-A,743
+marsilea/plotter/_images.py,sha256=gb0xIQhUch3rNAt3FfvuUoamSGEynoBBBky2eE754ec,9560
+marsilea/plotter/_seaborn.py,sha256=-0mtE-C_3zNjYWykJT5EMkJhU8FYCo12bBuJfbWvl3k,8264
+marsilea/plotter/_utils.py,sha256=Efhdk-TrrAanhbXRiEVWThMYvZ4vVHZMVYMs5X3JvIM,710
+marsilea/plotter/arc.py,sha256=44BKVGvDc_OpghfgEvaiVCovZe7_OwZiM20iepaRMFw,8139
+marsilea/plotter/area.py,sha256=zjjAhvgKHYe9rqzcseqZqhwfpgvzm0w2FRJ_vr9Fxm4,2650
+marsilea/plotter/bar.py,sha256=tXM5iR4cTkTrt55ff-aWoh7lxupKtA5vJ9Yn9hr7RkA,12067
+marsilea/plotter/base.py,sha256=TbnZDjm161RF5OlK4TCfhCFR9lM96MJUrvAk_xTk_kQ,20657
+marsilea/plotter/bio.py,sha256=34tucmxs4LM3TFZoGsrjnXTolyrzYaHVEiRe4dzDH68,5040
+marsilea/plotter/mesh.py,sha256=eUMXX9PNHJXf9O4wpcRgO6uEFKlpft1LwshHgMuojp8,24176
+marsilea/plotter/text.py,sha256=6S4mnAxLJLMkduKiyor03lPd86oTOJ5TojVREA9oU6s,37466
+oncoprinter/__init__.py,sha256=efshcAD1h9s-NVJj4HLU9-hXc_LtTeIrNYqLHl-sm_g,106
+oncoprinter/core.py,sha256=5KPnKW5ivlxPp14uJd0OtfTv-pXV2UEym8EbII2VCcw,11846
+oncoprinter/preset.py,sha256=mBk2tFCqoTj_1ZZKRYuv4j2I3NTBa6Swc9wjzbmxRVw,8238
+marsilea-0.4.3.dist-info/METADATA,sha256=edIeq4SMz38_uWLlkpiesySBghHd-1wEg72AYO7llFk,6576
+marsilea-0.4.3.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+marsilea-0.4.3.dist-info/licenses/LICENSE,sha256=2TLD8FnLJqXzg8YBRs7W3VZBwfWfp4ArDfBl-rn96Qc,1074
+marsilea-0.4.3.dist-info/RECORD,,

{marsilea-0.4.1.dist-info → marsilea-0.4.3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: flit 3.9.0
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

oncoprinter/__init__.py

@@ -0,0 +1,4 @@
+"""Draw oncoprint in Python"""
+
+from .core import OncoPrint
+from .preset import Rect, FracRect, FrameRect