plot-misc 2.3.0__py3-none-any.whl → 2.3.1__py3-none-any.whl

plot_misc/__init__.py

@@ -7,6 +7,12 @@ matplotlib `Figure`/`Axes` objects, so results can be further customised
 with familiar matplotlib methods. Per the package design callables are limited
 to creating illustrations, and should data be internally calculated this is
 done with options for user overwrites, while making the derived data available
-for inspection and re-use.
+for inspection and reuse.
 """
 from ._version import __version__
+
+__citation__ = (
+    "Schmidt AF, Hukerikar N, Finan C, van Vugt M. Effective visualization "
+    "of biomedical data using plot-misc. Bioinformatics Advances. "
+    "2026;6(1):vbag184. https://doi.org/10.1093/bioadv/vbag184"
+)

plot_misc/_version.py

@@ -1 +1 @@
-__version__ = '2.3.0'
+__version__ = '2.3.1'

plot_misc/example_data/example_datasets/string_data.txt

@@ -0,0 +1 @@
+hi!

plot_misc/example_data/examples.py

@@ -229,12 +229,12 @@ def help(name):
 @dataset
 def dummy_data():
     """A dummy dataset function that returns a small list.
-
+    
     Returns
     -------
     data : `list`
         A list of length 3 with ``['A', 'B', 'C']``
-
+    
     Notes
     -----
     This function is called ``dummy_data`` and has been decorated with a
@@ -253,7 +253,7 @@ def dummy_load_data():
     -------
     str_data : `str`
         A string of data loaded from an example data file.
-
+    
     Notes
     -----
     This function is called ``dummy_data`` and has been decorated with a
@@ -774,34 +774,34 @@ def load_survival_table(**kwargs):
     return table
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-@dataset
-def load_forest_preprocessed(**kwargs):
-    """
-    Loads the forest example data with subgroup colour and model shape
-    columns attached, ready for direct use by the forest plot.
+# @dataset
+# def load_forest_preprocessed(**kwargs):
+#     """
+#     Loads the forest example data with subgroup colour and model shape
+#     columns attached, ready for direct use by the forest plot.
     
-    Returns
-    -------
-    pd.DataFrame
-    """
-    # mapping literals (mirrors resources/examples/forestplot.ipynb cell 2)
-    col_dict = {
-        'wo T2DM/CVD': 'orangered',
-        'w T2DM': 'blueviolet',
-        'w T2DM & CVD': 'limegreen',
-    }
-    shape_dict = {
-        'PGS only': 'o',
-        'PGS plus': 's',
-        'PGS extended': 'H',
-    }
-    # base data (already carries the hardcoded ForestNames.y_col)
-    df = load_forest_data(**kwargs)
-    # attach colour and shape columns
-    df['col'] = df['subgroup_name'].map(col_dict)
-    df['shape'] = df['model'].map(shape_dict)
-    # return
-    return df
+#     Returns
+#     -------
+#     pd.DataFrame
+#     """
+#     # mapping literals (mirrors resources/examples/forestplot.ipynb cell 2)
+#     col_dict = {
+#         'wo T2DM/CVD': 'orangered',
+#         'w T2DM': 'blueviolet',
+#         'w T2DM & CVD': 'limegreen',
+#     }
+#     shape_dict = {
+#         'PGS only': 'o',
+#         'PGS plus': 's',
+#         'PGS extended': 'H',
+#     }
+#     # base data (already carries the hardcoded ForestNames.y_col)
+#     df = load_forest_data(**kwargs)
+#     # attach colour and shape columns
+#     df['col'] = df['subgroup_name'].map(col_dict)
+#     df['shape'] = df['model'].map(shape_dict)
+#     # return
+#     return df
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 @dataset

{plot_misc-2.3.0.dist-info → plot_misc-2.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plot-misc
-Version: 2.3.0
+Version: 2.3.1
 Summary: Various plotting archetypes built on top of matplotlib
 Author-email: A Floriaan Schmidt <floriaanschmidt@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -20,7 +20,7 @@ Requires-Dist: pandas>=1.3
 Requires-Dist: numpy>=1.21
 Requires-Dist: matplotlib>=3.5
 Requires-Dist: scipy>=1.5
-Requires-Dist: statsmodels>=0.1
+Requires-Dist: statsmodels>=0.12
 Requires-Dist: scikit-learn>=1.4
 Requires-Dist: adjustText>=1.3
 Requires-Dist: typing_extensions>=4; python_version < "3.11"
@@ -47,10 +47,10 @@ Requires-Dist: numpydoc; extra == "dev"
 Requires-Dist: docutils<0.21; extra == "dev"
 Dynamic: license-file
 
-<img src="https://schmidtaf.gitlab.io/plot-misc/_images/icon.png" alt="plot-misc icon" width="250"/>
+<img src="https://schmidtaf.gitlab.io/plot-misc/_images/fish.png" alt="plot-misc icon" width="250"/>
 
 # A collection of plotting functions
-__version__: `2.3.0`
+__version__: `2.3.1`
 
 This repository collects plotting modules written on top of `matplotlib`.
 The functions describe plotting archetypes intended to set up light-touch,
@@ -77,6 +77,25 @@ research:
 Please consult the **[documentation](https://SchmidtAF.gitlab.io/plot-misc/)** 
 for plot-misc.
 
+## Citation
+
+If you use this package in your research please cite the
+**[paper](https://academic.oup.com/bioinformaticsadvances/article/6/1/vbag184/8721292)**:
+
+```bibtex
+@article{Schmidt:2026,
+  author  = {Schmidt, Amand Floriaan and Hukerikar, Nikita and
+             Finan, Chris and van Vugt, Marion},
+  title   = {Effective visualization of biomedical data using plot-misc},
+  journal = {Bioinformatics Advances},
+  volume  = {6},
+  number  = {1},
+  pages   = {vbag184},
+  doi     = {10.1093/bioadv/vbag184},
+  year    = {2026}
+}
+```
+
 ## Installation 
 The package is available on PyPI, and conda, with the latest source code 
 available on gitlab. 
@@ -146,7 +165,7 @@ branches without reinstalling.
 Alternatively, you can install manually:
 ```bash
 python -m pip install -e .
-python .setup_git_hooks.py
+python .githooks/.setup_git_hooks.py
 ```
 
 #### Git Hooks Configuration
@@ -202,4 +221,8 @@ Please have a look at the examples in
 [resources](https://gitlab.com/SchmidtAF/plot-misc/-/tree/master/resources/examples)
 for some possible recipes. 
 
+## Icon
+
+The icon at the top of this README is a _mandarinfish_, widely regarded as one of
+the most colourful animals on the planet. 
 

{plot_misc-2.3.0.dist-info → plot_misc-2.3.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-plot_misc/__init__.py,sha256=3QUr_8ixNCHkqd6gnYmdbB-n2fe1pUrZjERtQwNzz5o,579
-plot_misc/_version.py,sha256=HkuhK2leBUgujkTPPE8VZAlHBDxmueEzVb4sz0_wlyQ,22
+plot_misc/__init__.py,sha256=9gmOKQn4BlRPhrNelBhlcHUeUg-RruLhHhO0UaUjRtA,807
+plot_misc/_version.py,sha256=0Ns5BhVD3XOEWhtSUJ76K319NapPiQfZKsWZRt-kZOk,22
 plot_misc/barchart.py,sha256=_4Fj8ypYi6Aehgv4b13Lh1zS1ee4z7OXrGo1P5QBshw,21925
 plot_misc/constants.py,sha256=SABaNQpTRXm4pMF_F6sdsBUvNVyb-WXQLT_YAmUgtuo,4530
 plot_misc/errors.py,sha256=ZbOZg1TbY-7dtPAsJNxIRsjlUfJg0vrx8kRPFsMClaQ,9637
@@ -11,7 +11,7 @@ plot_misc/piechart.py,sha256=nKT9Xr-rP9t8hv6ITb_0594AlzgfnAEdqkyCslLriLc,8613
 plot_misc/survival.py,sha256=_fKxaHSLjLU1Pq9KsxVqby5kXhl6QIsTM4sqq3hv6ak,25410
 plot_misc/volcano.py,sha256=4zAC4GH-sC5jJyDeHOTq9-3N-UgSldMKgutFs35KE4g,10298
 plot_misc/example_data/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-plot_misc/example_data/examples.py,sha256=T9jBdtQEbZKEWVoT0SJt8sJ5fTSdXpTqfDA6Y898s0g,31498
+plot_misc/example_data/examples.py,sha256=9F7xuJQGBu0WweoG719NdHPaOJaj5Dd1TzrqJXVC040,31564
 plot_misc/example_data/example_datasets/bar_points.tsv.gz,sha256=ppYQY01DXz77GzSANpwZ9N4zZvxQN5AiHmLsOhZ6cbk,255
 plot_misc/example_data/example_datasets/barchart.tsv.gz,sha256=9TVBaC7yuDuNzOQivTm-UxjmB_jyCfbv1twiL13WpOs,123
 plot_misc/example_data/example_datasets/calibration_bins.tsv.gz,sha256=7BQdx7Tx5zF6wSyyCTwjkSaELKywoykUpelWvxe5pxA,332
@@ -23,13 +23,14 @@ plot_misc/example_data/example_datasets/incidence_matrix_data.tsv.gz,sha256=A5IQ
 plot_misc/example_data/example_datasets/lollipop_data.tsv.gz,sha256=2EivSWOoYOxLKjFHgB86k9ln9xm3elTHd3eUI2tEwpg,820
 plot_misc/example_data/example_datasets/mace_associations.tsv.gz,sha256=oTtSzrOUbOqXap-wmA5QhJxKgj4O5nbpZ964J7AXBcw,1732
 plot_misc/example_data/example_datasets/net_benefit.tsv.gz,sha256=eW9ltgCj0smsq1_rGFbI0bujw4GkECfP89jIMk461iM,1323
+plot_misc/example_data/example_datasets/string_data.txt,sha256=GttBz476DDdb9k0IvA_gJ6cg_vDXrAUUDCof4SABVaI,4
 plot_misc/example_data/example_datasets/volcano.tsv.gz,sha256=Cd0J-VeiVPruUqdbPoMOCqDpOKZthITfKEKybsZ0qU8,41139
 plot_misc/utils/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 plot_misc/utils/colour.py,sha256=SfhjFcnvTQ-_zfstMqb0vMPyW3-pdPO4G3KJ7-BtQ4E,7715
 plot_misc/utils/formatting.py,sha256=RRXCSlGBv5SkshfZPnURcYy_QV9Zyu_ApbMdWxWRkAE,14018
 plot_misc/utils/utils.py,sha256=Ydu3TVwz48K6FhqSjFg0CbagJp0WRQbTRVgn6BQetfA,52113
-plot_misc-2.3.0.dist-info/licenses/LICENSE,sha256=TAKLZop-WRQ03q1liEZVOMPZOrVwR2ndHSdxC7j1YeU,779
-plot_misc-2.3.0.dist-info/METADATA,sha256=jX25HiLQ7cd2j-k2dUA4G1byqPWlmoDZKEXtwsXgW58,5813
-plot_misc-2.3.0.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
-plot_misc-2.3.0.dist-info/top_level.txt,sha256=WyOYx7sloAXvlDvWfFf57ZAf9PnKTWb0zqenkcZKkAE,10
-plot_misc-2.3.0.dist-info/RECORD,,
+plot_misc-2.3.1.dist-info/licenses/LICENSE,sha256=TAKLZop-WRQ03q1liEZVOMPZOrVwR2ndHSdxC7j1YeU,779
+plot_misc-2.3.1.dist-info/METADATA,sha256=ZAlUxBejWaIsGMzbQW5szU_pzuBSWWFZ32OQkzJ7WR8,6498
+plot_misc-2.3.1.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+plot_misc-2.3.1.dist-info/top_level.txt,sha256=WyOYx7sloAXvlDvWfFf57ZAf9PnKTWb0zqenkcZKkAE,10
+plot_misc-2.3.1.dist-info/RECORD,,

{plot_misc-2.3.0.dist-info → plot_misc-2.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (83.0.0)
+Generator: setuptools (84.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any