marsilea 0.3.3__tar.gz → 0.3.4__tar.gz

marsilea-0.3.4/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+yzheng@cemm.at.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

{marsilea-0.3.3 → marsilea-0.3.4}/PKG-INFO

@@ -1,12 +1,14 @@
 Metadata-Version: 2.1
 Name: marsilea
-Version: 0.3.3
+Version: 0.3.4
 Summary: Create x-layout visualization
 Author: Zhihang Zheng
 Author-email: Mr-Milk <yzheng@cemm.at>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Framework :: Matplotlib
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: matplotlib>=3.6

marsilea-0.3.4/docs/examples/Basics/plot_two_heatmap.py

@@ -0,0 +1,24 @@
+"""
+Two Heatmaps
+============
+
+This example shows how to plot two heatmaps side by side.
+
+"""
+
+# %%
+import numpy as np
+import marsilea as ma
+
+data1 = np.random.randint(0, 10, (20, 10))
+data2 = np.random.randint(0, 10, (10, 20))
+
+# %%
+h1 = ma.Heatmap(data1, linewidth=1, cmap="Reds", label="Heatmap 1")
+h1.add_dendrogram("left")
+h2 = ma.Heatmap(data2, linewidth=1, cmap="Blues", label="Heatmap 2")
+h2.add_dendrogram("right")
+(h1 + .2 + h2).render()
+
+# %%
+(h1 / .2 / h2).render()

{marsilea-0.3.3 → marsilea-0.3.4}/docs/examples/Gallery/plot_arc_diagram.py

@@ -6,7 +6,6 @@ This example shows how to create an arc diagram from a network.
 
 """
 
-import numpy as np
 import marsilea as ma
 import marsilea.plotter as mp
 

{marsilea-0.3.3 → marsilea-0.3.4}/docs/examples/Gallery/plot_available_plotters.py

@@ -56,7 +56,7 @@ plotters = {
     "Layers Mesh": ma.layers.LayersMesh(data2d, pieces=pieces),
 }
 
-canvas = ma.Heatmap(data2d, width=5, height=0, cmap="Oranges", label="Color Mesh")
+canvas = ma.ZeroHeightCluster(data2d, width=5)
 for title, plotter in plotters.items():
     canvas.add_bottom(plotter, name=title)
 
@@ -158,7 +158,7 @@ seqlogo = mp.SeqLogo(matrix, color_encode=colors)
 arc = mp.Arc([1, 2, 3, 4, 5], [(1, 5), (2, 3), (1, 2), (4, 5)],
              weights=weights, width=(2, 5), colors="#534D56")
 
-canvas4 = ma.Heatmap(rng.standard_normal((10, 5)), width=4, height=0)
+canvas4 = ma.ZeroHeightCluster(rng.standard_normal((10, 5)), width=4)
 canvas4.add_top(seqlogo, size=2, name="Sequence Logo")
 canvas4.add_top(arc, size=1, pad=.2, name="Arc Diagram")
 canvas4.render()

{marsilea-0.3.3 → marsilea-0.3.4}/docs/examples/Gallery/plot_mouse_embryo.py

@@ -109,6 +109,7 @@ for n in cell_types:
     y_ax.text(0.5, 0, n, va="top", ha="center", rotation=90, transform=y_ax.transAxes)
 
 
+# sphinx_gallery_ignore_start
 #%%
 if '__file__' in globals():
     from pathlib import Path
@@ -118,3 +119,4 @@ if '__file__' in globals():
     save_path = Path(__file__).parent / "imgs"
     plt.savefig(save_path / "mouse_embryo.svg", bbox_inches="tight")
     plt.savefig(save_path / "mouse_embryo.png", dpi=300, bbox_inches="tight")
+# sphinx_gallery_ignore_end

{marsilea-0.3.3 → marsilea-0.3.4}/docs/examples/Gallery/plot_seqalign.py

@@ -7,7 +7,6 @@ import numpy as np
 import pandas as pd
 
 import marsilea as ma
-import marsilea.plotter as mp
 import matplotlib as mpl
 
 # sphinx_gallery_start_ignore

{marsilea-0.3.3 → marsilea-0.3.4}/docs/examples/Gallery/plot_upset.py

@@ -8,7 +8,7 @@ IMDB Top 1000 Movies
 from matplotlib import pyplot as plt
 
 import marsilea as ma
-from marsilea.upset import UpsetData, Upset
+from marsilea.upset import UpsetData
 
 # sphinx_gallery_start_ignore
 import mpl_fontkit as fk

marsilea-0.3.4/docs/examples/Plotters/plot_area.py

@@ -0,0 +1,18 @@
+"""
+Area
+====
+
+:class:`~marsilea.plotter.Area` is a plotter for drawing area plot.
+
+"""
+
+# %%
+from marsilea.plotter import Area
+
+# %%
+import numpy as np
+import matplotlib.pyplot as plt
+
+_, ax = plt.subplots()
+data = np.random.randint(0, 10, 10) + 1
+Area(data).render(ax)

{marsilea-0.3.3 → marsilea-0.3.4}/docs/source/api/index.rst

@@ -119,6 +119,18 @@ Declarative API Cheat Sheet
 
             wb.save("output.png", dpi=300)
 
+    * - :code:`+`
+      - Two canvas side by side, number will be added as white space
+      - .. code-block:: python
+
+            (wb1 + 1 + wb2).render()
+
+    * - :code:`/`
+      - Two canvas top and bottom, number will be added as white space
+      - .. code-block:: python
+
+            (wb1 / 1 / wb2).render()
+
 
 High-Level Visualizations
 =========================
@@ -216,10 +228,11 @@ Other plots
     :template: autosummary.rst
     :nosignatures:
 
+    Area
+    Arc
     Numbers
     StackBar
     CenterBar
-    Arc
     SeqLogo
 
 
@@ -239,8 +252,8 @@ Text Label
 
 
 
-Base Class
-==========
+Main Canvas
+===========
 
 
 .. currentmodule:: marsilea.base
@@ -254,9 +267,11 @@ Base Class
     LegendMaker
     ZeroWidth
     ZeroHeight
+    ZeroWidthCluster
+    ZeroHeightCluster
 
 Layout Engine
--------------
+=============
 
 .. currentmodule:: marsilea.layout
 .. autosummary::
@@ -269,7 +284,7 @@ Layout Engine
 
 
 Data Manipulation
------------------
+=================
 
 .. currentmodule:: marsilea
 .. autosummary::
@@ -280,7 +295,7 @@ Data Manipulation
     Deformation
 
 Render plan
------------
+===========
 
 .. currentmodule:: marsilea.plotter.base
 .. autosummary::

{marsilea-0.3.3 → marsilea-0.3.4}/docs/source/conf.py

@@ -91,7 +91,7 @@ def matplotlib_tight_scraper(*args, **kwargs):
 
 
 intersphinx_mapping = {
-    'scipy': ('https://docs.scipy.org/doc', None),
+    'scipy': ('http://docs.scipy.org/doc/scipy/', None),
     'seaborn': ('https://seaborn.pydata.org/', None),
     'matplotlib': ('https://matplotlib.org/stable', None),
     'legendkit': ('https://legendkit.readthedocs.io/en/stable', None),

{marsilea-0.3.3 → marsilea-0.3.4}/pyproject.toml

@@ -10,7 +10,11 @@ authors = [
 ]
 license = {file = "LICENSE"}
 readme = "README.md"
-classifiers = ["License :: OSI Approved :: MIT License"]
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Framework :: Matplotlib",
+]
 dynamic = ["version", "description"]
 requires-python = ">=3.8"
 urls = {Home="https://github.com/Marsilea-viz/marsilea"}

{marsilea-0.3.3 → marsilea-0.3.4}/src/marsilea/__init__.py

@@ -1,10 +1,12 @@
 """Create x-layout visualization"""
 
-__version__ = "0.3.3"
+__version__ = "0.3.4"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation
-from .base import WhiteBoard, ClusterBoard, ZeroWidth, ZeroHeight
+from .base import (WhiteBoard, ClusterBoard,
+                   ZeroWidth, ZeroHeight,
+                   ZeroWidthCluster, ZeroHeightCluster)
 from .dataset import load_data
 from .dendrogram import Dendrogram, GroupDendrogram
 from .heatmap import Heatmap, SizedHeatmap, CatHeatmap

{marsilea-0.3.3 → marsilea-0.3.4}/src/marsilea/base.py

@@ -1403,3 +1403,50 @@ class ClusterBoard(WhiteBoard):
         # add row and col dendrogram
         self._render_dendrogram()
         self._render_legend()
+
+
+class ZeroWidthCluster(ClusterBoard):
+    """
+    A utility class to initialize a canvas \
+    with zero width and cluster data
+
+    Parameters
+    ----------
+    cluster_data : ndarray
+        The cluster data
+    height : float
+        The height of the main canvas in inches
+    name : str
+        The name of the main canvas
+    margin : float, 4-tuple
+        The margin of the main canvas in inches
+
+    """
+
+    def __init__(self, cluster_data, height, name=None, margin=0.2):
+        super().__init__(cluster_data=cluster_data, width=0, height=height,
+                         name=name, margin=margin, init_main=False)
+
+
+class ZeroHeightCluster(ClusterBoard):
+    """
+    A utility class to initialize a canvas \
+    with zero height and cluster data
+
+    Parameters
+    ----------
+    cluster_data : ndarray
+        The cluster data
+    width : float
+        The width of the main canvas in inches
+    name : str
+        The name of the main canvas
+    margin : float, 4-tuple
+        The margin of the main canvas in inches
+
+
+    """
+
+    def __init__(self, cluster_data, width, name=None, margin=0.2):
+        super().__init__(cluster_data=cluster_data, width=width, height=0,
+                         name=name, margin=margin, init_main=False)

{marsilea-0.3.3 → marsilea-0.3.4}/src/marsilea/layers.py

@@ -360,6 +360,7 @@ class Marker(Piece):
         self.size = size
         m = MarkerStyle(marker)
         self.path = m.get_path().transformed(m.get_transform())
+        self.marker = marker
 
     def draw(self, x, y, w, h, ax):
         c = self.draw_center(x, y, w, h)

{marsilea-0.3.3 → marsilea-0.3.4}/src/marsilea/plotter/area.py

@@ -26,6 +26,20 @@ class Area(StatsBase):
         Additional configurations for the area plot, \
         see :func:`matplotlib.pyplot.fill_between`
 
+    Examples
+    --------
+    .. plot::
+        :context: close-figs
+
+        import numpy as np
+        import matplotlib.pyplot as plt
+
+        from marsilea.plotter import Area
+
+        _, ax = plt.subplots()
+        data = np.random.randint(0, 10, 10) + 1
+        Area(data).render(ax)
+
     """
 
     def __init__(self, data, color=None, add_outline=True, alpha=.4,
@@ -46,6 +60,7 @@ class Area(StatsBase):
         self.kws = kwargs
 
         self.set_data(data)
+        self.set_label(label, label_loc, label_props)
         if group_kws is not None:
             self.set_group_params(group_kws)
 
@@ -56,7 +71,7 @@ class Area(StatsBase):
         if gp is None:
             gp = {}
 
-        fill_options = {'colo': self.color, 'alpha': self.alpha, **self.kws, **gp}
+        fill_options = {'color': self.color, 'alpha': self.alpha, **self.kws, **gp}
         line_options = {'color': self.linecolor, 'linewidth': self.linewidth, **gp}
 
         x = np.arange(len(data))