Set grid behind in plot_settings

aaanalysis/plotting/plot_settings_.py

@@ -155,27 +155,38 @@ def plot_settings(font_scale: float = 1,
     if show_options:
         print(plt.rcParams.keys)
 
-    # Set embedded fonts in PDF
+    # Set all values to matplotlib default
     mpl.rcParams.update(mpl.rcParamsDefault)
-    mpl.rcParams["pdf.fonttype"] = 42
 
     # Change only font style
     if adjust_only_font:
+        mpl.rcParams['pdf.fonttype'] = 42  # Set embedded fonts in PDF via TrueType
+        mpl.rcParams['ps.fonttype'] = 42
+        mpl.rcParams['svg.fonttype'] = 'none'
         plt.rcParams["font.family"] = "sans-serif"
         plt.rcParams["font.sans-serif"] = font
         return
 
     # Apply all changes
     sns.set_context("talk", font_scale=font_scale)
+
+    # Handle storing of vectorized figure format
+    mpl.rcParams['pdf.fonttype'] = 42  # Set embedded fonts in PDF via TrueType
+    mpl.rcParams['ps.fonttype'] = 42
+    mpl.rcParams['svg.fonttype'] = 'none'
+
     # Font settings
     plt.rcParams["font.family"] = "sans-serif"
     plt.rcParams["font.sans-serif"] = font
     font_settings = {'family': 'sans-serif', "weight": "bold"} if weight_bold else {'family': 'sans-serif'}
     mpl.rc('font', **font_settings)
+
     # Grid
     plt.rcParams["axes.grid.axis"] = grid_axis
     plt.rcParams["axes.grid"] = grid
     plt.rcParams["grid.linewidth"] = 1 if weight_bold else 0.8
+    plt.rcParams["axes.axisbelow"] = True
+
     # Adjust weight of text and lines
     if weight_bold:
         plt.rcParams["axes.labelweight"] = "bold"
@@ -210,11 +221,6 @@ def plot_settings(font_scale: float = 1,
     else:
         set_tick_size(axis="y", major_size=default_major_size, minor_size=default_minor_size)
 
-    # Handle storing of vectorized figure format
-    mpl.rcParams['pdf.fonttype'] = 42   # TrueType
-    mpl.rcParams['ps.fonttype'] = 42
-    mpl.rcParams['svg.fonttype'] = 'none'
-
     # Additional adjustments
     if adjust_further_elements:
         # Error bars

docs/build/html/_sources/generated/plotting_prelude.rst.txt

@@ -1,4 +1,4 @@
-Plotting prelude
+Plotting Prelude
 ================
 
 These are some of our utility plotting functions to make

docs/build/html/generated/aaanalysis.plot_settings.html

@@ -130,7 +130,7 @@
 <h1>aaanalysis.plot_settings<a class="headerlink" href="#aaanalysis-plot-settings" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="aaanalysis.plot_settings">
-<span class="sig-prename descclassname"><span class="pre">aaanalysis.</span></span><span class="sig-name descname"><span class="pre">plot_settings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">font_scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Arial'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight_bold</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="n"><span class="pre">adjust_only_font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjust_further_elements</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="n"><span class="pre">grid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'y'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_settings_.py#L42-L225"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_settings" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">aaanalysis.</span></span><span class="sig-name descname"><span class="pre">plot_settings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">font_scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Arial'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight_bold</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="n"><span class="pre">adjust_only_font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjust_further_elements</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="n"><span class="pre">grid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'y'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks_x</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_ticks_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_ticks_y</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_settings_.py#L42-L231"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_settings" title="Permalink to this definition"></a></dt>
 <dd><p>Configures general settings for plot visualization.</p>
 <p>This function modifies the global settings of <a class="reference external" href="https://matplotlib.org/stable/index.html#module-matplotlib" title="(in Matplotlib v3.8.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">matplotlib</span></code></a> and <code class="xref py py-mod docutils literal notranslate"><span class="pre">seaborn</span></code> libraries.
 It adjusts font embedding for vector formats like PDF and SVG, ensuring compatibility and

docs/build/html/generated/plotting_prelude.html

@@ -2,20 +2,20 @@
 <html class="writer-html5" lang="en" >
 <head>
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18: http://docutils.sourceforge.net/" />
-<meta property="og:title" content="Plotting prelude" />
+<meta property="og:title" content="Plotting Prelude" />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="generated/plotting_prelude.html" />
 <meta property="og:site_name" content="AAanalysis" />
 <meta property="og:description" content="These are some of our utility plotting functions to make publication-ready visualizations with a view extra lines of code. Let us first make all imports and create some data The default seaborn out..." />
 <meta property="og:image:width" content="1146" />
 <meta property="og:image:height" content="600" />
-<meta property="og:image" content="/_images/social_previews/summary_generated_plotting_prelude_53cbcc27.png" />
+<meta property="og:image" content="/_images/social_previews/summary_generated_plotting_prelude_11ec0463.png" />
 <meta property="og:image:alt" content="These are some of our utility plotting functions to make publication-ready visualizations with a view extra lines of code. Let us first make all imports and..." />
 <meta name="description" content="These are some of our utility plotting functions to make publication-ready visualizations with a view extra lines of code. Let us first make all imports and create some data The default seaborn out..." />
 <meta name="twitter:card" content="summary_large_image" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Plotting prelude &mdash; AAanalysis</title>
+  <title>Plotting Prelude &mdash; AAanalysis</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/copybutton.css" type="text/css" />
@@ -79,7 +79,7 @@
 <li class="toctree-l1 current"><a class="reference internal" href="../tutorials.html">Tutorials</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="../tutorials.html#quick-start">Quick start</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="tutorial1_quick_start.html">Quick Start with AAanalysis</a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Plotting prelude</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Plotting Prelude</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../tutorials.html#further-tutorials">Further Tutorials</a></li>
@@ -110,7 +110,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="../tutorials.html">Tutorials</a></li>
-      <li class="breadcrumb-item active">Plotting prelude</li>
+      <li class="breadcrumb-item active">Plotting Prelude</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/generated/plotting_prelude.rst" class="fa fa-github"> Edit on GitHub</a>
       </li>
@@ -121,7 +121,7 @@
            <div itemprop="articleBody">
 
   <section id="plotting-prelude">
-<h1>Plotting prelude<a class="headerlink" href="#plotting-prelude" title="Permalink to this heading"></a></h1>
+<h1>Plotting Prelude<a class="headerlink" href="#plotting-prelude" title="Permalink to this heading"></a></h1>
 <p>These are some of our utility plotting functions to make
 publication-ready visualizations with a view extra lines of code.</p>
 <p>Let us first make all imports and create some data</p>

docs/build/html/generated/tutorial1_quick_start.html

@@ -41,7 +41,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Plotting prelude" href="plotting_prelude.html" />
+    <link rel="next" title="Plotting Prelude" href="plotting_prelude.html" />
     <link rel="prev" title="Tutorials" href="../tutorials.html" /> 
 </head>
 
@@ -79,7 +79,7 @@
 <li class="toctree-l1 current"><a class="reference internal" href="../tutorials.html">Tutorials</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="../tutorials.html#quick-start">Quick start</a><ul class="current">
 <li class="toctree-l3 current"><a class="current reference internal" href="#">Quick Start with AAanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="plotting_prelude.html">Plotting prelude</a></li>
+<li class="toctree-l3"><a class="reference internal" href="plotting_prelude.html">Plotting Prelude</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../tutorials.html#further-tutorials">Further Tutorials</a></li>
@@ -774,7 +774,7 @@ <h3>Explainable AI on individual level<a class="headerlink" href="#explainable-a
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="../tutorials.html" class="btn btn-neutral float-left" title="Tutorials" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="plotting_prelude.html" class="btn btn-neutral float-right" title="Plotting prelude" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="plotting_prelude.html" class="btn btn-neutral float-right" title="Plotting Prelude" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

docs/build/html/generated/tutorial2a_data_loader.html

@@ -42,7 +42,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Scale Loading Tutorial" href="tutorial2b_scales_loader.html" />
-    <link rel="prev" title="Plotting prelude" href="plotting_prelude.html" /> 
+    <link rel="prev" title="Plotting Prelude" href="plotting_prelude.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -907,7 +907,7 @@ <h2>Loading of protein benchmarks: Positive-Unlabeled (PU) datasets<a class="hea
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="plotting_prelude.html" class="btn btn-neutral float-left" title="Plotting prelude" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="plotting_prelude.html" class="btn btn-neutral float-left" title="Plotting Prelude" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="tutorial2b_scales_loader.html" class="btn btn-neutral float-right" title="Scale Loading Tutorial" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

docs/build/html/tutorials.html

@@ -6,12 +6,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="tutorials.html" />
 <meta property="og:site_name" content="AAanalysis" />
-<meta property="og:description" content="Quick start: Quick Start with AAanalysis, Plotting prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
+<meta property="og:description" content="Quick start: Quick Start with AAanalysis, Plotting Prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
 <meta property="og:image:width" content="1146" />
 <meta property="og:image:height" content="600" />
-<meta property="og:image" content="/_images/social_previews/summary_tutorials_2c8534e9.png" />
-<meta property="og:image:alt" content="Quick start: Quick Start with AAanalysis, Plotting prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
-<meta name="description" content="Quick start: Quick Start with AAanalysis, Plotting prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
+<meta property="og:image" content="/_images/social_previews/summary_tutorials_156b1d6c.png" />
+<meta property="og:image:alt" content="Quick start: Quick Start with AAanalysis, Plotting Prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
+<meta name="description" content="Quick start: Quick Start with AAanalysis, Plotting Prelude. Further Tutorials: Data Loading Tutorial, Scale Loading Tutorial." />
 <meta name="twitter:card" content="summary_large_image" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -79,7 +79,7 @@
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorials</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#quick-start">Quick start</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="generated/tutorial1_quick_start.html">Quick Start with AAanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="generated/plotting_prelude.html">Plotting prelude</a></li>
+<li class="toctree-l3"><a class="reference internal" href="generated/plotting_prelude.html">Plotting Prelude</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#further-tutorials">Further Tutorials</a><ul>
@@ -130,7 +130,7 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Permalink to thi
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="generated/tutorial1_quick_start.html">Quick Start with AAanalysis</a></li>
-<li class="toctree-l1"><a class="reference internal" href="generated/plotting_prelude.html">Plotting prelude</a></li>
+<li class="toctree-l1"><a class="reference internal" href="generated/plotting_prelude.html">Plotting Prelude</a></li>
 </ul>
 </div>
 </section>

docs/source/generated/plotting_prelude.rst

@@ -1,4 +1,4 @@
-Plotting prelude
+Plotting Prelude
 ================
 
 These are some of our utility plotting functions to make