marsilea 0.4.8__py3-none-any.whl → 0.5.0rc1__py3-none-any.whl

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Files changed (6) hide show
  1. marsilea/__init__.py +1 -1
  2. marsilea/heatmap.py +6 -3
  3. {marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/METADATA +17 -17
  4. {marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/RECORD +6 -6
  5. {marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/WHEEL +0 -0
  6. {marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/licenses/LICENSE +0 -0
marsilea/__init__.py CHANGED
@@ -1,6 +1,6 @@
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  """Declarative creation of composable visualization"""
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- __version__ = "0.4.8"
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+ __version__ = "0.5.0rc1"
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  import marsilea.plotter as plotter
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  from ._deform import Deformation
marsilea/heatmap.py CHANGED
@@ -50,6 +50,7 @@ class Heatmap(ClusterBoard):
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  height=None,
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  cluster_data=None,
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  init_main=True,
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+ legend=True,
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  **kwargs,
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  ):
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  if cluster_data is None:
@@ -80,7 +81,7 @@ class Heatmap(ClusterBoard):
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  )
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  name = get_plot_name(name, "main", mesh.__class__.__name__)
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  mesh.set(name=name)
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- self.add_layer(mesh)
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+ self.add_layer(mesh, legend=legend)
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  class CatHeatmap(ClusterBoard):
@@ -109,6 +110,7 @@ class CatHeatmap(ClusterBoard):
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  name=None,
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  width=None,
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  height=None,
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+ legend=True,
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  cluster_data=None,
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  linewidth=0,
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  linecolor="white",
@@ -128,7 +130,7 @@ class CatHeatmap(ClusterBoard):
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  super().__init__(cluster_data, width=width, height=height, name=name)
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  name = get_plot_name(name, "main", mesh.__class__.__name__)
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  mesh.set(name=name)
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- self.add_layer(mesh)
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+ self.add_layer(mesh, legend=legend)
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  class SizedHeatmap(ClusterBoard):
@@ -156,6 +158,7 @@ class SizedHeatmap(ClusterBoard):
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  name=None,
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  width=None,
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  height=None,
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+ legend=True,
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  **kwargs,
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  ):
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  if cluster_data is None:
@@ -166,4 +169,4 @@ class SizedHeatmap(ClusterBoard):
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  super().__init__(cluster_data, width=width, height=height, name=name)
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  mesh = SizedMesh(size=size, color=color, **kwargs)
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- self.add_layer(mesh)
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+ self.add_layer(mesh, legend=legend)
{marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/METADATA RENAMED
@@ -1,10 +1,11 @@
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  Metadata-Version: 2.4
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  Name: marsilea
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- Version: 0.4.8
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- Dynamic: Summary
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+ Version: 0.5.0rc1
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+ Summary: Declarative creation of composable visualizations
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  Project-URL: Home, https://github.com/Marsilea-viz/marsilea
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+ Project-URL: Documentation, https://marsilea.readthedocs.io
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  Author: Zhihang Zheng
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- Author-email: Mr-Milk <yzheng@cemm.at>
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+ Author-email: Yimin Zheng <yzheng@cemm.at>
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  License: The MIT License (MIT)
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  Copyright (c) 2024 Mr-Milk
@@ -30,6 +31,8 @@ License-File: LICENSE
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  Classifier: Framework :: Matplotlib
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  Classifier: License :: OSI Approved :: MIT License
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  Classifier: Programming Language :: Python :: 3
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+ Classifier: Topic :: Scientific/Engineering
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+ Classifier: Topic :: Scientific/Engineering :: Visualization
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  Requires-Python: >=3.8
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  Requires-Dist: legendkit
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  Requires-Dist: matplotlib>=3.6
@@ -38,20 +41,6 @@ Requires-Dist: pandas[parquet]
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  Requires-Dist: platformdirs
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  Requires-Dist: scipy
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  Requires-Dist: seaborn
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- Provides-Extra: dev
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- Requires-Dist: icecream; extra == 'dev'
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- Requires-Dist: mpl-fontkit; extra == 'dev'
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- Requires-Dist: numpydoc; extra == 'dev'
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- Requires-Dist: pre-commit; extra == 'dev'
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- Requires-Dist: pydata-sphinx-theme; extra == 'dev'
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- Requires-Dist: pytest; extra == 'dev'
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- Requires-Dist: python-hmr; extra == 'dev'
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- Requires-Dist: ruff; extra == 'dev'
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- Requires-Dist: scikit-learn; extra == 'dev'
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- Requires-Dist: sphinx; extra == 'dev'
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- Requires-Dist: sphinx-copybutton; extra == 'dev'
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- Requires-Dist: sphinx-design; extra == 'dev'
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- Requires-Dist: sphinx-gallery; extra == 'dev'
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  Description-Content-Type: text/markdown
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  <p align="center">
@@ -66,6 +55,7 @@ Description-Content-Type: text/markdown
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  ![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
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  ![Conda Version](https://img.shields.io/conda/vn/conda-forge/marsilea?style=flat-square&logo=anaconda&logoColor=white&color=%2344A833)
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  ![PyPI - License](https://img.shields.io/pypi/l/marsilea?color=FFD43B&style=flat-square)
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+ [![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03469--3-blue?color=0098FF&style=flat-square)](https://doi.org/10.1186/s13059-024-03469-3)
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  # Marsilea: Declarative creation of composable visualization!
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@@ -104,6 +94,16 @@ and then create a bar chart to show the expression of genes in different cell ty
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  A visualization contains multiple plots is called a composable visualization.
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  In Marsilea, we employ a declarative approach for user to create composable visualization incrementally.
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+ ## Citation
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+
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+ If you use Marsilea in your research, please cite the following:
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+
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+ > Marsilea: an intuitive generalized paradigm for composable visualizations
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+ >
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+ > Yimin Zheng, Zhihang Zheng, André F. Rendeiro & Edwin Cheung
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+ >
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+ > _Genome Biology_ 2025 Jan 06. DOI: [10.1186/s13059-017-1382-0](https://doi.org/10.1186/s13059-024-03469-3)
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+
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  ## Examples
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  <table>
{marsilea-0.4.8.dist-info → marsilea-0.5.0rc1.dist-info}/RECORD RENAMED
@@ -1,11 +1,11 @@
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- marsilea/__init__.py,sha256=4gKfHq47N9IViIzNNmV_ESrbrDwd1Lx2HnVonhJH42c,595
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+ marsilea/__init__.py,sha256=_eGLcXHTDSPWqHXJEpLBbU9NJ9V2Obemv-GsjsrZOmU,598
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  marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
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  marsilea/_deform.py,sha256=QRz4OGXMsQzbiIkC3ASzZayMPhHhoFsEK38oBzSeQG8,14440
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  marsilea/base.py,sha256=WTQ1L2Geyt4KjrWWQMSrS-0Z2do2R7FOdBx5_2W8Z7w,51206
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  marsilea/dataset.py,sha256=Qh8k1DhTiwP_Me709CkpNwRaYLDzlenRTIk0U6D58_g,4631
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  marsilea/dendrogram.py,sha256=Ung43zseybZKzTEvH5P_ge3WGfsr7i7qsX7YEVDlC74,15590
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  marsilea/exceptions.py,sha256=wN5ElUZxuaJKSnnwWdkNx6P-Oc16dzSuaRPbRKWIBEM,1046
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- marsilea/heatmap.py,sha256=UhRcBFhx1JKrtndZPvQCDaiMt8Pb314PT1BtL-JndCY,4208
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+ marsilea/heatmap.py,sha256=8Wo1NxFTBp1a7NOISmer0yQYWWgf51Xsvjav1h1vTYk,4316
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  marsilea/layers.py,sha256=puXLlGGpEqAzaTqadpgpsYmIDPH33WyyHIuysRSqFZQ,12163
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  marsilea/layout.py,sha256=yNuGvIDfWjbCksQZO-4aUWSA78LJwBBKF5Z5cthC6fM,39741
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  marsilea/upset.py,sha256=JnqV9HYYpoeLt-6yMy0HN_PUSgV-ENasf6vq6HsX3cI,30393
@@ -25,7 +25,7 @@ marsilea/plotter/text.py,sha256=6S4mnAxLJLMkduKiyor03lPd86oTOJ5TojVREA9oU6s,3746
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  oncoprinter/__init__.py,sha256=efshcAD1h9s-NVJj4HLU9-hXc_LtTeIrNYqLHl-sm_g,106
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  oncoprinter/core.py,sha256=5KPnKW5ivlxPp14uJd0OtfTv-pXV2UEym8EbII2VCcw,11846
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  oncoprinter/preset.py,sha256=mBk2tFCqoTj_1ZZKRYuv4j2I3NTBa6Swc9wjzbmxRVw,8238
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- marsilea-0.4.8.dist-info/METADATA,sha256=NAJopsdO64Z8Mtl5HQjEzZ2wm51Jv2eCjkD7UhKOqQc,6866
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- marsilea-0.4.8.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- marsilea-0.4.8.dist-info/licenses/LICENSE,sha256=2TLD8FnLJqXzg8YBRs7W3VZBwfWfp4ArDfBl-rn96Qc,1074
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- marsilea-0.4.8.dist-info/RECORD,,
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+ marsilea-0.5.0rc1.dist-info/METADATA,sha256=iQf49kl4rB5G0nDjejE6-BGqZ3y8z0pLs7tLrWEeGUs,6996
29
+ marsilea-0.5.0rc1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ marsilea-0.5.0rc1.dist-info/licenses/LICENSE,sha256=2TLD8FnLJqXzg8YBRs7W3VZBwfWfp4ArDfBl-rn96Qc,1074
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+ marsilea-0.5.0rc1.dist-info/RECORD,,