[MERGE] v.0.6.0

See changelog.md

.github/workflows/python-package.yml

@@ -12,11 +12,11 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', 3.11]
 
     steps:
     - uses: actions/checkout@v3

.gitignore

@@ -3,8 +3,12 @@ __pycache__
 build
 dist
 
+statannot.egg-info/
 statannot.egg-info/dependency_links.txt
 statannot.egg-info/PKG-INFO
 statannot.egg-info/requires.txt
 statannot.egg-info/SOURCES.txt
 statannot.egg-info/top_level.txt
+
+# IDE files
+.idea/

CHANGELOG.md

@@ -1,5 +1,25 @@
-## v0.5
-### v0.5.0
+## v0.6
+### v0.6.0
+#### Features
+- Add option to skip annotation of non-significant results 
+  (PR [#95](https://github.com/trevismd/statannotations/pull/95) by 
+  [sepro](https://github.com/sepro))
+
+#### Fixes
+- Fix keeping annotation with reduced ylim (
+  PR [#116](https://github.com/trevismd/statannotations/issues/116) by
+  [amkorb](https://github.com/amkorb))
+- Fix pvalue legend (usually for NS range)
+
+#### Additional testing and documentation:
+  - PR [#84](https://github.com/trevismd/statannotations/pull/84) by
+    [JasonMendoza2008 ](https://github.com/JasonMendoza2008)
+  - PR [#86](https://github.com/trevismd/statannotations/pull/86) by 
+    [mbhall88](https://github.com/mbhall88)
+  - PR [#117](https://github.com/trevismd/statannotations/pull/117) by
+    [tathey1](https://github.com/tathey1)
+
+## v0.5.0
 - Add scipy's Brunner-Munzel test
 - Fix applying statannotations for non-string group labels (Issue 
   [#65](https://github.com/trevismd/statannotations/issues/65))

README.md

@@ -62,14 +62,15 @@ corresponding branch).
 - Optionally, custom p-values can be given as input.
       In this case, no statistical test is performed, but **corrections for
       multiple testing can be applied.**
+- It is also possible to hide non statistically significant annotations
 - Any text can be used as annotation
 - And various fixes (see
   [CHANGELOG.md](https://github.com/trevismd/statannotations/blob/master/CHANGELOG.md)).
 
 ## Installation
 
 From version 0.3.0 on, the package is distributed on PyPi.
-The latest stable release (v0.5.0) can be downloaded and installed with:
+The latest stable release (v0.6.0) can be downloaded and installed with:
 ```bash
 pip install statannotations
 ```
@@ -90,9 +91,9 @@ pip install -r requirements.txt .
 
 ## Important note
 
-**! Seaborn ≥ v0.12 is not officially supported, we know there are at least 
-some bugs. Issues can still be reported (and upvoted) in order to plan further
-development to support these versions. Also see 
+**! Seaborn ≥ v0.12 and pandas 2 are not officially supported, we know there are
+at least some bugs. Issues can still be reported (and upvoted) in order to plan 
+further development to support these versions. Also see 
 [discussion](https://github.com/trevismd/statannotations/discussions/81)**.
 
 ## Usage
@@ -142,7 +143,7 @@ annotator.apply_and_annotate()
 + numpy >= 1.12.1
 + seaborn >= 0.9,<0.12
 + matplotlib >= 2.2.2
-+ pandas >= 0.23.0
++ pandas >= 0.23.0,<2.0.0
 + scipy >= 1.1.0
 + statsmodels (optional, for multiple testing corrections)
 
@@ -171,7 +172,7 @@ Bibtex
   month        = oct,
   year         = 2022,
   publisher    = {Zenodo},
-  version      = {v0.5},
+  version      = {v0.6},
   doi          = {10.5281/zenodo.7213391},
   url          = {https://doi.org/10.5281/zenodo.7213391}
 }
@@ -181,7 +182,7 @@ Example
 Florian Charlier, Marc Weber, Dariusz Izak, Emerson Harkin, Marcin Magnus, 
 Joseph Lalli, Louison Fresnais, Matt Chan, Nikolay Markov, Oren Amsalem, 
 Sebastian Proost, Agamemnon Krasoulis, getzze, & Stefan Repplinger. (2022). 
-Statannotations (v0.5). Zenodo. https://doi.org/10.5281/zenodo.7213391
+Statannotations (v0.6). Zenodo. https://doi.org/10.5281/zenodo.7213391
 ```
 
 ## Contributing

docs/build/html/_sources/modules.rst.txt

@@ -5,3 +5,4 @@ statannotations
    :maxdepth: 4
 
    statannotations
+   custom-test

docs/build/html/_sources/statannotations.rst.txt

@@ -20,6 +20,8 @@ statannotations.Annotation module
    :undoc-members:
    :show-inheritance:
 
+.. _Annotator_module:
+
 statannotations.Annotator module
 --------------------------------
 

docs/build/html/_sources/statannotations.stats.rst.txt

@@ -20,6 +20,8 @@ statannotations.stats.StatResult module
    :undoc-members:
    :show-inheritance:
 
+.. _StatTest_module:
+
 statannotations.stats.StatTest module
 -------------------------------------
 

docs/build/html/genindex.html

@@ -211,6 +211,8 @@ <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="statannotations.stats.html#statannotations.stats.utils.check_alpha">check_alpha() (in module statannotations.stats.utils)</a>
+</li>
+      <li><a href="statannotations.html#statannotations.Annotation.Annotation.check_data_stat_result">check_data_stat_result() (statannotations.Annotation.Annotation method)</a>
 </li>
       <li><a href="statannotations.html#statannotations.utils.check_is_in">check_is_in() (in module statannotations.utils)</a>
 </li>
@@ -337,6 +339,10 @@ <h2 id="I">I</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="statannotations.html#statannotations.utils.InvalidParametersError">InvalidParametersError</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="statannotations.stats.html#statannotations.stats.StatResult.StatResult.is_significant">is_significant (statannotations.stats.StatResult.StatResult property)</a>
 </li>
   </ul></td>
 </tr></table>

docs/build/html/index.html

@@ -163,6 +163,7 @@ <h1>Welcome to statannotations’s documentation!<a class="headerlink" href="#we
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">statannotations</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="statannotations.html">statannotations package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="custom-test.html">Extending to other statistical functions</a></li>
 </ul>
 </li>
 </ul>

docs/build/html/modules.html

@@ -91,6 +91,7 @@
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">statannotations</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="statannotations.html">statannotations package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="custom-test.html">Extending to other statistical functions</a></li>
 </ul>
 </li>
 </ul>
@@ -187,6 +188,7 @@ <h1>statannotations<a class="headerlink" href="#statannotations" title="Permalin
 <li class="toctree-l2"><a class="reference internal" href="statannotations.html#module-statannotations">Module contents</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="custom-test.html">Extending to other statistical functions</a></li>
 </ul>
 </div>
 </div>

docs/build/html/statannotations.html

@@ -104,6 +104,7 @@
 <li class="toctree-l3"><a class="reference internal" href="#module-statannotations">Module contents</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="custom-test.html">Extending to other statistical functions</a></li>
 </ul>
 </li>
 </ul>
@@ -204,6 +205,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">statannotations.Annotation.</span></span><span class="sig-name descname"><span class="pre">Annotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span> </span><a class="reference internal" href="statannotations.stats.html#statannotations.stats.StatResult.StatResult" title="statannotations.stats.StatResult.StatResult"><span class="pre">statannotations.stats.StatResult.StatResult</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">formatter</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#statannotations.PValueFormat.Formatter" title="statannotations.PValueFormat.Formatter"><span class="pre">statannotations.PValueFormat.Formatter</span></a><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#statannotations.Annotation.Annotation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Holds data, linked structs and an optional Formatter.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="statannotations.Annotation.Annotation.check_data_stat_result">
+<span class="sig-name descname"><span class="pre">check_data_stat_result</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#statannotations.Annotation.Annotation.check_data_stat_result" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="statannotations.Annotation.Annotation.formatted_output">
 <em class="property"><span class="pre">property</span> </em><span class="sig-name descname"><span class="pre">formatted_output</span></span><a class="headerlink" href="#statannotations.Annotation.Annotation.formatted_output" title="Permalink to this definition">¶</a></dt>
@@ -223,7 +229,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 </div>
 <div class="section" id="module-statannotations.Annotator">
-<span id="statannotations-annotator-module"></span><h2>statannotations.Annotator module<a class="headerlink" href="#module-statannotations.Annotator" title="Permalink to this headline">¶</a></h2>
+<span id="statannotations-annotator-module"></span><span id="annotator-module"></span><h2>statannotations.Annotator module<a class="headerlink" href="#module-statannotations.Annotator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="statannotations.Annotator.Annotator">
 <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">statannotations.Annotator.</span></span><span class="sig-name descname"><span class="pre">Annotator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pairs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'boxplot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hue</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hue_order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">engine</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'seaborn'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">plot_params</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#statannotations.Annotator.Annotator" title="Permalink to this definition">¶</a></dt>
@@ -314,6 +320,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </dd>
 </dl>
 </li>
+<li><dl class="simple">
+<dt><cite>hide_non_significant</cite>: hide annotations for non-significant pair</dt><dd><p>comparisons</p>
+</dd>
+</dl>
+</li>
 <li><p><cite>line_height</cite>: in axes fraction coordinates</p></li>
 <li><p><cite>line_offset</cite></p></li>
 <li><p><cite>line_offset_to_group</cite></p></li>

docs/build/html/statannotations.stats.html

@@ -41,6 +41,7 @@
 
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Extending to other statistical functions" href="custom-test.html" />
     <link rel="prev" title="statannotations package" href="statannotations.html" /> 
 </head>
 
@@ -103,6 +104,7 @@
 <li class="toctree-l3"><a class="reference internal" href="statannotations.html#module-statannotations">Module contents</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="custom-test.html">Extending to other statistical functions</a></li>
 </ul>
 </li>
 </ul>
@@ -241,6 +243,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <em class="property"><span class="pre">property</span> </em><span class="sig-name descname"><span class="pre">formatted_output</span></span><a class="headerlink" href="#statannotations.stats.StatResult.StatResult.formatted_output" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
+<dl class="py property">
+<dt class="sig sig-object py" id="statannotations.stats.StatResult.StatResult.is_significant">
+<em class="property"><span class="pre">property</span> </em><span class="sig-name descname"><span class="pre">is_significant</span></span><a class="headerlink" href="#statannotations.stats.StatResult.StatResult.is_significant" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
 <dl class="py property">
 <dt class="sig sig-object py" id="statannotations.stats.StatResult.StatResult.significance_suffix">
 <em class="property"><span class="pre">property</span> </em><span class="sig-name descname"><span class="pre">significance_suffix</span></span><a class="headerlink" href="#statannotations.stats.StatResult.StatResult.significance_suffix" title="Permalink to this definition">¶</a></dt>
@@ -250,7 +257,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 </div>
 <div class="section" id="module-statannotations.stats.StatTest">
-<span id="statannotations-stats-stattest-module"></span><h2>statannotations.stats.StatTest module<a class="headerlink" href="#module-statannotations.stats.StatTest" title="Permalink to this headline">¶</a></h2>
+<span id="statannotations-stats-stattest-module"></span><span id="stattest-module"></span><h2>statannotations.stats.StatTest module<a class="headerlink" href="#module-statannotations.stats.StatTest" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="statannotations.stats.StatTest.StatTest">
 <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">statannotations.stats.StatTest.</span></span><span class="sig-name descname"><span class="pre">StatTest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Callable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_long_name</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_short_name</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stat_name</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'Stat'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">float</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#statannotations.stats.StatTest.StatTest" title="Permalink to this definition">¶</a></dt>
@@ -357,6 +364,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
           </div>
           <footer>
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+        <a href="custom-test.html" class="btn btn-neutral float-right" title="Extending to other statistical functions" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
         <a href="statannotations.html" class="btn btn-neutral float-left" title="statannotations package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 

docs/source/custom-test.rst

@@ -0,0 +1,4 @@
+Extending to other statistical functions
+****************************************
+
+.. include:: ../../statannotations/stats/README.rst

docs/source/modules.rst

@@ -5,3 +5,4 @@ statannotations
    :maxdepth: 4
 
    statannotations
+   custom-test

docs/source/statannotations.rst

@@ -20,6 +20,8 @@ statannotations.Annotation module
    :undoc-members:
    :show-inheritance:
 
+.. _Annotator_module:
+
 statannotations.Annotator module
 --------------------------------
 

docs/source/statannotations.stats.rst

@@ -20,6 +20,8 @@ statannotations.stats.StatResult module
    :undoc-members:
    :show-inheritance:
 
+.. _StatTest_module:
+
 statannotations.stats.StatTest module
 -------------------------------------
 

requirements.txt

@@ -1,7 +1,7 @@
 numpy>=1.12.1
 seaborn>=0.9.0,<0.12
 matplotlib>=2.2.2
-pandas>=0.23.0
+pandas>=0.23.0,<2.0.0
 scipy>=1.1.0
 statsmodels
-packaging
+packaging

statannotations/Annotation.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Union
 
 from statannotations.PValueFormat import Formatter
@@ -43,3 +44,10 @@ def print_labels_and_content(self, sep=" vs. "):
                                  for struct in self.structs)
 
         print(f"{labels_string}: {self.formatted_output}")
+
+    def check_data_stat_result(self):
+        if not isinstance(self.data, StatResult):
+            warnings.warn("Annotation data has incorrect class." +
+                          "Should be StatResult. Cannot annotate current pair.")
+            return False
+        return True