ridgeplot-py 0.2.3__tar.gz → 0.2.7__tar.gz

{ridgeplot_py-0.2.3 → ridgeplot_py-0.2.7}/PKG-INFO

@@ -1,21 +1,22 @@
 Metadata-Version: 2.1
 Name: ridgeplot-py
-Version: 0.2.3
+Version: 0.2.7
 Summary: Plotting ridgeplots with matplotlib
 License: MIT
 Author: Douglas Wu
 Author-email: wckdouglas@gmail.com
-Requires-Python: >=3.8,<4.0
+Requires-Python: >=3.9,<4.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Provides-Extra: dev
-Requires-Dist: matplotlib (>=3.1.3,<4.0.0)
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: matplotlib (>=3.8,<4.0)
 Requires-Dist: more-itertools (>=8.9.0,<9.0.0)
 Requires-Dist: numpy (>=1.21.1,<2.0.0)
+Requires-Dist: pandas (>=2.2.2,<3.0.0)
+Requires-Dist: poetry (>=1.8.3,<2.0.0)
 Requires-Dist: scipy (>=1.8.0,<2.0.0)
 Description-Content-Type: text/markdown
 

{ridgeplot_py-0.2.3 → ridgeplot_py-0.2.7}/pyproject.toml

@@ -1,35 +1,38 @@
 [tool.poetry]
 name = "ridgeplot-py"
-version = "0.2.3" # managed by poetry-dynamic-versioning
+version = "0.2.7"                                   # managed by poetry-dynamic-versioning
 description = "Plotting ridgeplots with matplotlib"
 authors = ["Douglas Wu <wckdouglas@gmail.com>"]
 license = "MIT"
-packages = [
-    {"include" = "ridgeplot"}
-]
+packages = [{ "include" = "ridgeplot" }]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.9"
 scipy = "^1.8.0"
-matplotlib = "^3.1.3"
+matplotlib = "^3.8"
 more-itertools = "^8.9.0"
 numpy = "^1.21.1"
+pandas = "^2.2.2"
+poetry = "^1.8.3"
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
 pytest = "^6.2.5"
 pytest-cov = "^2.12.1"
-mypy = "^0.910"
-black = "22.3.0"
+mypy = "^0.990"
 ruff = "^0.0.290"
+pre-commit = "^3.7.0"
 
 [tool.poetry-dynamic-versioning]
 enable = false
 vcs = "git"
-metadata= false
+metadata = false
 bump = true
 style = "pep440"
-pattern  = "^(?P<base>\\d+\\.\\d+\\.\\d+)(-?((?P<stage>[a-zA-Z]+)\\.?(?P<revision>\\d+)?))?"
+pattern = "^(?P<base>\\d+\\.\\d+\\.\\d+)(-?((?P<stage>[a-zA-Z]+)\\.?(?P<revision>\\d+)?))?"
 format-jinja = """
     {%- set ns = namespace(version=base) -%}
     {%- for i in range(distance) -%}
@@ -42,20 +45,17 @@ format-jinja = """
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
 build-backend = "poetry_dynamic_versioning.backend"
 
-[tool.poetry.extras]
-dev = ["pytest", "pytest-cov", "mypy", "ruff", "black"]
-
 [tool.mypy]
 plugins = "numpy.typing.mypy_plugin"
+ignore_missing_imports = true
+strict_optional = true
+check_untyped_defs = true
 
 [[tool.mypy.overrides]]
-module = [
-    "matplotlib.*",
-    "scipy.*"
-]
-ignore_missing_imports = true
+module = ["matplotlib.*", "scipy.*"]
+ignore_errors = true
+
 
 [tool.ruff]
 line-length = 120
 select = ['E', 'F', 'W', 'I']
-

{ridgeplot_py-0.2.3 → ridgeplot_py-0.2.7}/ridgeplot/colors.py

@@ -3,11 +3,13 @@ for matplotlib plots and a collections of color palettes.
 """
 
 from collections import OrderedDict
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Tuple
 
 import matplotlib.axes
 import matplotlib.patches as mpatches
 from matplotlib import legend
+from matplotlib.cm import get_cmap
+from matplotlib.colors import to_hex
 
 ColorPalette: Dict[str, List[str]] = dict(
     # 1. maximum
@@ -139,6 +141,7 @@ class ColorEncoder:
 
     Example:
         ```
+        >>> from ridgeplot.colors import ColorEncoder, ColorPalette
         >>> categorical_vector = ['group a','group b','group c','group a']
         >>> colors = ColorPalette["okabeito"]
         >>> ce = ColorEncoder()
@@ -248,7 +251,12 @@ class ColorEncoder:
         self.fit(categories, colors=colors)
         return self.transform(categories)
 
-    def show_legend(self, ax: matplotlib.axes, sort: bool = False, **kwargs: Dict[str, Any]) -> legend.Legend:
+    def show_legend(
+        self,
+        ax: matplotlib.axes._axes.Axes,
+        sort: bool = False,
+        **kwargs: Dict[str, Any],
+    ) -> legend.Legend:
         """
         Adding matplotlib legend describing the color encoder to a matplotlib ax object
 
@@ -266,3 +274,17 @@ class ColorEncoder:
         pat = [mpatches.Patch(color=col, label=lab) for lab, col in self.encoder.items()]
         lgd = ax.legend(handles=pat, **kwargs)
         return lgd
+
+
+def get_cmap_color_values(cmap_name: str) -> Tuple[str, str]:
+    """
+    Get color values for the min and max color in a color map
+
+    Args:
+        cmap_name: color map name (e.g. viridis)
+
+    Returns:
+        hex code for the min and max color
+    """
+    cmap = get_cmap(cmap_name)
+    return to_hex(cmap(0.0)), to_hex(cmap(1.0))

ridgeplot_py-0.2.7/ridgeplot/dotted_heatmap.py

@@ -0,0 +1,69 @@
+"""
+for most of the part, this is copied from:
+https://stackoverflow.com/questions/59381273/heatmap-with-circles-indicating-size-of-population
+"""
+
+from __future__ import annotations
+
+from typing import Optional
+
+import matplotlib.axes
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+from matplotlib.collections import PatchCollection
+
+
+def dotted_heatmap(
+    data: pd.DataFrame,
+    ax: matplotlib.axes._axes.Axes,
+    cmap: str = "cividis",
+    circle_size: Optional[float] = None,
+):
+    """
+    Plotting dotted heatmap
+
+    Example:
+        ```
+        >>> import matplotlib.pyplot as plt
+        >>> from ridgeplot.dotted_heatmap import dotted_heatmap
+        >>> fig = plt.figure()
+        >>> ax = fig.add_subplot(111)
+        >>> data = pd.DataFrame(
+        ...    np.random.randn(n, n),
+        ...    index=[f"feature{i}" for i in range(n)],
+        ...    columns=[f"sample{i}" for i in range(n)],
+        ... )
+        >>> dotted_heatmap(data=data,ax=ax, cmap="viridis")
+        ```
+
+    Args:
+        data: data to plot
+        ax: matplotlib ax object
+        cmap: cmap value, defaults to "cividis"
+        circle_size: raidus of the circles,
+            if None, we will use relaive sizes, defaults to None
+    """
+    nrows, ncols = data.shape
+    x, y = np.meshgrid(np.arange(ncols), np.arange(nrows))
+    radii = data.values / 2 / data.values.max()
+    # radius is relative if circle_size is None
+    circles = [
+        plt.Circle((j, i), radius=circle_size if circle_size is not None else r)
+        for r, j, i in zip(radii.flat, x.flat, y.flat)
+    ]
+    col = PatchCollection(circles, array=data.values.flatten(), cmap=cmap)
+    ax.add_collection(col)
+
+    ax.set_xticks(np.arange(ncols))
+    ax.set_xticklabels(data.columns)
+    ax.set_yticks(np.arange(nrows))
+    ax.set_yticklabels(data.index)
+
+    ax.set_xticks(np.arange(ncols + 1) - 0.5, minor=True)
+    ax.set_yticks(np.arange(nrows + 1) - 0.5, minor=True)
+    ax.grid(which="minor", alpha=0.5, color="white")
+    ax.tick_params(left=False, bottom=False)
+    for d in ["top", "bottom", "left", "right"]:
+        ax.spines[d].set(alpha=0.5)
+    plt.colorbar(col)

{ridgeplot_py-0.2.3 → ridgeplot_py-0.2.7}/ridgeplot/ridge_plot.py

@@ -1,6 +1,7 @@
 """This module contains the main function to plot
 [ridgeplots](https://clauswilke.com/blog/2017/09/15/goodbye-joyplots/).
 """
+
 from __future__ import annotations
 
 from typing import Optional
@@ -18,7 +19,7 @@ class RidgePlotError(Exception):
 
 
 def ridgeplot(
-    ax: matplotlib.axes,
+    ax: matplotlib.axes._axes.Axes,
     data: dict[str, list[float]],
     xlim: Optional[tuple[float, float]] = None,
     fill_colors: Optional[list[str]] = None,
@@ -33,6 +34,7 @@ def ridgeplot(
         ```
         >>> import numpy as np
         >>> import matplotlib.pyplot as plt
+        >>> from ridgeplot.ridge_plot import ridgeplot
 
         >>> data = {}
         >>> for i in range(10):

ridgeplot_py-0.2.3/setup.py

@@ -1,33 +0,0 @@
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-packages = \
-['ridgeplot']
-
-package_data = \
-{'': ['*']}
-
-install_requires = \
-['matplotlib>=3.1.3,<4.0.0',
- 'more-itertools>=8.9.0,<9.0.0',
- 'numpy>=1.21.1,<2.0.0',
- 'scipy>=1.8.0,<2.0.0']
-
-setup_kwargs = {
-    'name': 'ridgeplot-py',
-    'version': '0.2.3',
-    'description': 'Plotting ridgeplots with matplotlib',
-    'long_description': '# ridgeplot-py #\n\n[![CI](https://github.com/wckdouglas/ridgeplot-py/actions/workflows/ci.yaml/badge.svg)](https://github.com/wckdouglas/ridgeplot-py/actions/workflows/ci.yaml) [![codecov](https://codecov.io/gh/wckdouglas/ridgeplot-py/branch/main/graph/badge.svg?token=2owCGZa1K4)](https://codecov.io/gh/wckdouglas/ridgeplot-py) [![PyPI version](https://badge.fury.io/py/ridgeplot-py.svg)](https://badge.fury.io/py/ridgeplot-py) [![conda-forge](https://anaconda.org/conda-forge/ridgeplot-py/badges/version.svg)](https://anaconda.org/conda-forge/ridgeplot-py)\n\n\nThis is a simple module for plotting [ridgeplot](https://clauswilke.com/blog/2017/09/15/goodbye-joyplots/) with the [scipy ecosystem](https://www.scipy.org/about.html).\n\nRidgeplot is a great data visualization technique to compare distributions from multiple groups at the same time, and was first introduced in 2017 as joy plot:\n\n<blockquote class="twitter-tweet"><p lang="en" dir="ltr">I hereby propose that we call these &quot;joy plots&quot; <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://t.co/uuLGpQLAwY">https://t.co/uuLGpQLAwY</a></p>&mdash; Jenny Bryan (@JennyBryan) <a href="https://twitter.com/JennyBryan/status/856674638981550080?ref_src=twsrc%5Etfw">April 25, 2017</a></blockquote> \n\n[ridgeplot-py](https://pypi.org/project/ridgeplot-py/) provides a simple API to produce matplotlib-compatible ridgeplots, as well as a handy [ColorEncoder](https://github.com/wckdouglas/ridgeplot-py/blob/0198628ce0622e2e7f4f4e9284165d5d09324ca9/ridgeplot/colors.py#L117) class with scikit-learn syntax for manipulating color annotations in a consistent way [through out manuscripts or presentations].\n\n## Install ##\n\n```bash\ngit clone git@github.com:wckdouglas/ridgeplot-py.git\ncd ridgeplot-py\npython setup.py install \n```\n\nor via conda:\n\n```bash\nconda install -c conda-forge ridgeplot-py\n```\n\nor via pypi:\n\n```bash\npip install ridgeplot-py\n```\n\n## Usage ##\n\n```python\nfrom ridgeplot import ridgeplot\nfrom ridgeplot.colors import ColorEncoder, ColorPalette\nimport numpy as np\nimport matplotlib.pyplot as plt\n\n# mocking some data\n# the input data should be a dict of\n# - keys: group names for the distributions\n# - values: list of values \ndata = {}\nfor i in range(8):\n    data[\'data_{}\'.format(i)] = np.random.randn(100) * (i+1)\n\n# make the plot\nfig = plt.figure()\nax = fig.add_subplot(111)\nridgeplot(\n    ax, \n    data, \n    xlim=(-20,20), \n    label_size=15\n)\n```\n\n![img](https://raw.githubusercontent.com/wckdouglas/ridgeplot-py/main/img/ridgeplot.png)\n\n\n## Example ##\n\nA [notebook](https://github.com/wckdouglas/ridgeplot-py/blob/main/Example.ipynb) showing quick howto is included in this repo!\n\n\n## Build on Apple silicon ##\n\nscipy may cause error and may be able to solved by the [this stackoverflow answer](https://stackoverflow.com/a/71764028):\n\n```\nbrew install openblas\nexport OPENBLAS="$(brew --prefix openblas)" \npoetry install\n```\n',
-    'author': 'Douglas Wu',
-    'author_email': 'wckdouglas@gmail.com',
-    'maintainer': 'None',
-    'maintainer_email': 'None',
-    'url': 'None',
-    'packages': packages,
-    'package_data': package_data,
-    'install_requires': install_requires,
-    'python_requires': '>=3.8,<4.0',
-}
-
-
-setup(**setup_kwargs)