Add plotting prelude

aaanalysis/plotting/plot_gcfs_.py

@@ -29,6 +29,9 @@ def plot_gcfs():
         >>> plt.tight_layout()
         >>> plt.show()
 
+    See Also
+    --------
+    * Our `Plotting Prelude <plotting_prelude.html>`_.
     """
     # Get the current plotting context
     current_context = sns.plotting_context()

aaanalysis/plotting/plot_get_cdict_.py

@@ -36,6 +36,9 @@ def plot_get_cdict(name: str = "DICT_COLOR") -> dict:
         >>> plt.tight_layout()
         >>> plt.show()
 
+    See Also
+    --------
+    * Our `Plotting Prelude <plotting_prelude.html>`_.
     """
     list_names = [ut.STR_DICT_COLOR, ut.STR_DICT_CAT]
     if name not in list_names:

aaanalysis/plotting/plot_get_clist_.py

@@ -39,7 +39,7 @@ def plot_get_clist(n_colors: int = 3) -> List[str]:
 
     See Also
     --------
-    * Example notebooks in `Plotting Prelude <plotting_prelude.html>`_.
+    * The example notebooks in `Plotting Prelude <plotting_prelude.html>`_.
     * `Matplotlib color names <https://matplotlib.org/stable/gallery/color/named_colors.html>`_
     * :func:`seaborn.color_palette` function to generate a color palette in seaborn.
     """

aaanalysis/plotting/plot_get_cmap_.py

@@ -93,7 +93,7 @@ def plot_get_cmap(name: str = "CPP",
 
     See Also
     --------
-    * Example notebooks in `Plotting Prelude <plotting_prelude.html>`_.
+    * Our `Plotting Prelude <plotting_prelude.html>`_.
     * `Matplotlib color names <https://matplotlib.org/stable/gallery/color/named_colors.html>`_
     * :func:`seaborn.color_palette` function to generate a color palette in seaborn.
     * :func:`seaborn.light_palette function` to generate a lighter color palettes.

aaanalysis/plotting/plot_set_legend_.py

@@ -192,7 +192,7 @@ def plot_set_legend(ax: Optional[plt.Axes] = None,
                     marker: Optional[Union[str, int, list]] = None,
                     marker_size: Union[int, float, List[Union[int, float]]] = 10,
                     marker_linestyle: Union[str, list] = "-",
-                    hatch: Optional[str] = None,
+                    hatch: Optional[Union[str, List[str]]] = None,
                     # Title
                     title: str = None,
                     title_align_left: bool = True,
@@ -284,6 +284,7 @@ def plot_set_legend(ax: Optional[plt.Axes] = None,
 
     See Also
     --------
+    * More examples in `Plotting Prelude <plotting_prelude.html>`_.
     * `Matplotlib markers <https://matplotlib.org/stable/api/markers_api.html>`.
     * `Linestyles of markers <https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html>`
     * `Hatches <https://matplotlib.org/stable/gallery/shapes_and_collections/hatch_style_reference.html>`_ filling patterns.

aaanalysis/plotting/plot_settings_.py

@@ -25,15 +25,6 @@ def check_font(font="Arial"):
         raise ValueError(error_message)
 
 
-def check_fig_format(fig_format="pdf"):
-    """"""
-    list_fig_formats = ['eps', 'jpg', 'jpeg', 'pdf', 'pgf', 'png', 'ps',
-                        'raw', 'rgba', 'svg', 'svgz', 'tif', 'tiff', 'webp']
-    ut.check_str(name="fig_format", val=fig_format)
-    if fig_format not in list_fig_formats:
-        raise ValueError(f"'fig_format' should be one of following: {list_fig_formats}")
-
-
 def check_grid_axis(grid_axis="y"):
     list_grid_axis = ["y", "x", "both"]
     if grid_axis not in list_grid_axis:
@@ -50,7 +41,6 @@ def set_tick_size(axis=None, major_size=None, minor_size=None):
 # II Main functions
 def plot_settings(font_scale: float = 1,
                   font: str = "Arial",
-                  fig_format: str = "pdf",
                   weight_bold: bool = True,
                   adjust_only_font: bool = False,
                   adjust_further_elements: bool = True,
@@ -67,16 +57,15 @@ def plot_settings(font_scale: float = 1,
     Configures general settings for plot visualization.
 
     This function modifies the global settings of :mod:`matplotlib` and :mod:`seaborn` libraries.
-    PDFs are embedded such that they can be edited using image editing software.
+    It adjusts font embedding for vector formats like PDF and SVG, ensuring compatibility and
+    editability across various viewers and editing software.
 
     Parameters
     ----------
     font_scale
        Scaling factor to scale the size of font elements. Consistent with :func:`seaborn.set_context`.
     font
        Name of text font. Common options are 'Arial', 'Verdana', 'Helvetica', or 'DejaVu Sans' (Matplotlib default).
-    fig_format
-       Specifies the file format for saving plots. Most backends support png, pdf, ps, eps and svg.
     weight_bold
        If ``True``, font and line elements are bold.
     adjust_only_font
@@ -138,13 +127,13 @@ def plot_settings(font_scale: float = 1,
 
     See Also
     --------
+    * More examples in `Plotting Prelude <plotting_prelude.html>`_.
     * :func:`seaborn.set_context`, where ``font_scale`` is utilized.
     * :data:`matplotlib.rcParams`, which manages the global settings in :mod:`matplotlib`.
     """
     # Check input
     ut.check_number_range(name="font_scale", val=font_scale, min_val=0, just_int=False)
     check_font(font=font)
-    check_fig_format(fig_format=fig_format)
     check_grid_axis(grid_axis=grid_axis)
     args_bool = {"weight_bold": weight_bold, "adjust_only_font": adjust_only_font,
                  "adjust_further_elements": adjust_further_elements, "grid": grid,
@@ -186,6 +175,7 @@ def plot_settings(font_scale: float = 1,
     # Grid
     plt.rcParams["axes.grid.axis"] = grid_axis
     plt.rcParams["axes.grid"] = grid
+    plt.rcParams["grid.linewidth"] = 1 if weight_bold else 0.8
     # Adjust weight of text and lines
     if weight_bold:
         plt.rcParams["axes.labelweight"] = "bold"
@@ -204,7 +194,6 @@ def plot_settings(font_scale: float = 1,
     short_minor_size = 2
     no_major_size = 0
     no_minor_size = 0
-
     # Set x ticks
     if no_ticks or no_ticks_x:
         set_tick_size(axis="x", major_size=no_major_size, minor_size=no_minor_size)
@@ -221,11 +210,10 @@ def plot_settings(font_scale: float = 1,
     else:
         set_tick_size(axis="y", major_size=default_major_size, minor_size=default_minor_size)
 
-    # Handle figure format
-    if fig_format == "pdf":
-        mpl.rcParams['pdf.fonttype'] = 42
-    elif "svg" in fig_format:
-        mpl.rcParams['svg.fonttype'] = 'none'
+    # 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:

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

@@ -1,7 +1,91 @@
 Plotting prelude
 ================
 
-This is a short overview of our utility plotting functions to make
-publication-ready visualizations with a view extra lines of code using
-the three following functions:
+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
+
+.. code:: ipython2
+
+    import matplotlib.pyplot as plt
+    import seaborn as sns
+    import warnings
+    warnings.simplefilter(action='ignore', category=FutureWarning) 
+    
+    data = {'Classes': ['Class A', 'Class B', 'Class C'], 'Values': [23, 27, 43]}
+
+The default seaborn output with removed top and right spines looks like
+this:
+
+.. code:: ipython2
+
+    sns.barplot(x='Classes', y='Values', data=data)
+    sns.despine()
+    plt.title("Seaborn default")
+    plt.tight_layout()
+    plt.show()
+
+
+
+.. image:: output_3_0.png
+
+
+Just call our ``aa.plot_setting`` function with our optimized color set
+to get this:
+
+.. code:: ipython2
+
+    import aaanalysis as aa
+    colors = aa.plot_get_clist()
+    aa.plot_settings()
+    sns.barplot(x='Classes', y='Values', data=data, palette=colors)
+    sns.despine()
+    plt.title("Adjusted by AAanalysis 1")
+    plt.tight_layout()
+    plt.show()
+
+
+
+.. image:: output_5_0.png
+
+
+The settings can be easily adjusted and colors are provided for up to 9
+classes:
+
+.. code:: ipython2
+
+    data = {'Classes': ['Class A', 'Class B', 'Class C', "Class D", "Class E"], 'Values': [23, 27, 43, 9, 14]}
+    colors = aa.plot_get_clist(n_colors=5)
+    aa.plot_settings(no_ticks_x=True, short_ticks_y=True, grid=True, grid_axis="y")
+    sns.barplot(x='Classes', y='Values', data=data, palette=colors)
+    sns.despine()
+    plt.title("Adjusted by AAanalysis 2")
+    plt.tight_layout()
+    plt.show()
+
+
+
+.. image:: output_7_0.png
+
+
+Retrieve the set font size and create an independent legend like this:
+
+.. code:: ipython2
+
+    data = {'Classes': ['Class A', 'Class B', 'Class C', "Class D", "Class E"], 'Values': [23, 27, 43, 9, 14]}
+    colors = aa.plot_get_clist(n_colors=5)
+    aa.plot_settings(no_ticks_x=True, short_ticks_y=True)
+    sns.barplot(x='Classes', y='Values', data=data, palette=colors, hatch=["/", "/", "/", ".", "."])
+    fontsize = aa.plot_gcfs()
+    sns.despine()
+    plt.title("Adjusted by AAanalysis 3")
+    dict_color = {"Group 1": "black", "Group 2": "black"}
+    aa.plot_set_legend(dict_color=dict_color, ncol=1, x=0.7, y=0.9, hatch=["/", "."])
+    plt.tight_layout()
+    plt.show()
+
+
+
+.. image:: output_9_0.png
 

docs/build/html/generated/aaanalysis.plot_gcfs.html

@@ -130,7 +130,7 @@
 <h1>aaanalysis.plot_gcfs<a class="headerlink" href="#aaanalysis-plot-gcfs" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="aaanalysis.plot_gcfs">
-<span class="sig-prename descclassname"><span class="pre">aaanalysis.</span></span><span class="sig-name descname"><span class="pre">plot_gcfs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_gcfs_.py#L7-L36"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_gcfs" 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_gcfs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_gcfs_.py#L7-L39"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_gcfs" title="Permalink to this definition"></a></dt>
 <dd><p>Gets current font size.</p>
 <p>This font size can be set by <a class="reference internal" href="aaanalysis.plot_settings.html#aaanalysis.plot_settings" title="aaanalysis.plot_settings"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot_settings()</span></code></a> function.</p>
 <div class="admonition-examples admonition">
@@ -154,6 +154,12 @@ <h1>aaanalysis.plot_gcfs<a class="headerlink" href="#aaanalysis-plot-gcfs" title
 <img alt="../_images/aaanalysis-plot_gcfs-1.png" class="plot-directive" src="../_images/aaanalysis-plot_gcfs-1.png" />
 </figure>
 </div>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<ul class="simple">
+<li><p>Our <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
+</ul>
+</div>
 </dd></dl>
 
 </section>

docs/build/html/generated/aaanalysis.plot_get_cdict.html

@@ -130,7 +130,7 @@
 <h1>aaanalysis.plot_get_cdict<a class="headerlink" href="#aaanalysis-plot-get-cdict" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="aaanalysis.plot_get_cdict">
-<span class="sig-prename descclassname"><span class="pre">aaanalysis.</span></span><span class="sig-name descname"><span class="pre">plot_get_cdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DICT_COLOR'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_get_cdict_.py#L5-L46"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_get_cdict" 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_get_cdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DICT_COLOR'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/breimanntools/aaanalysis/tree/master/aaanalysis/plotting/plot_get_cdict_.py#L5-L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#aaanalysis.plot_get_cdict" title="Permalink to this definition"></a></dt>
 <dd><p>Returns color dictionarie specified for AAanalysis.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -170,6 +170,12 @@ <h1>aaanalysis.plot_get_cdict<a class="headerlink" href="#aaanalysis-plot-get-cd
 <img alt="../_images/aaanalysis-plot_get_cdict-1.png" class="plot-directive" src="../_images/aaanalysis-plot_get_cdict-1.png" />
 </figure>
 </div>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<ul class="simple">
+<li><p>Our <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
+</ul>
+</div>
 </dd></dl>
 
 </section>

docs/build/html/generated/aaanalysis.plot_get_clist.html

@@ -165,7 +165,7 @@ <h1>aaanalysis.plot_get_clist<a class="headerlink" href="#aaanalysis-plot-get-cl
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <ul class="simple">
-<li><p>Example notebooks in <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
+<li><p>The example notebooks in <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
 <li><p><a class="reference external" href="https://matplotlib.org/stable/gallery/color/named_colors.html">Matplotlib color names</a></p></li>
 <li><p><a class="reference external" href="https://seaborn.pydata.org/generated/seaborn.color_palette.html#seaborn.color_palette" title="(in seaborn v0.12.2)"><code class="xref py py-func docutils literal notranslate"><span class="pre">seaborn.color_palette()</span></code></a> function to generate a color palette in seaborn.</p></li>
 </ul>

docs/build/html/generated/aaanalysis.plot_get_cmap.html

@@ -174,7 +174,7 @@ <h1>aaanalysis.plot_get_cmap<a class="headerlink" href="#aaanalysis-plot-get-cma
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <ul class="simple">
-<li><p>Example notebooks in <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
+<li><p>Our <a class="reference external" href="plotting_prelude.html">Plotting Prelude</a>.</p></li>
 <li><p><a class="reference external" href="https://matplotlib.org/stable/gallery/color/named_colors.html">Matplotlib color names</a></p></li>
 <li><p><a class="reference external" href="https://seaborn.pydata.org/generated/seaborn.color_palette.html#seaborn.color_palette" title="(in seaborn v0.12.2)"><code class="xref py py-func docutils literal notranslate"><span class="pre">seaborn.color_palette()</span></code></a> function to generate a color palette in seaborn.</p></li>
 <li><p><code class="xref py py-func docutils literal notranslate"><span class="pre">seaborn.light_palette</span> <span class="pre">function()</span></code> to generate a lighter color palettes.</p></li>