update docs

docs/build/doctrees/nbsphinx/notebooks/dotHeatmap.ipynb

@@ -18,7 +18,8 @@
     "plt.rcParams['pdf.fonttype']=42\n",
     "sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap/\"))\n",
     "import PyComplexHeatmap\n",
-    "from PyComplexHeatmap import *"
+    "from PyComplexHeatmap import *\n",
+    "use_pch_style() # or plt.style.use('default') to restore default style"
    ]
   },
   {

docs/build/doctrees/nbsphinx/notebooks/get_started.ipynb

@@ -10,15 +10,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 12,
    "id": "57e9d138-6953-4426-83c3-f4682fca20aa",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "1.7.2.dev0+g8abf70a.d20240415\n"
+      "1.7.7.dev0+gddb18da.d20240909\n"
      ]
     }
    ],

docs/build/doctrees/nbsphinx/notebooks/oncoPrint.ipynb

@@ -16,6 +16,7 @@
    "outputs": [],
    "source": [
     "import os,sys\n",
+    "import pandas as pd\n",
     "%matplotlib inline\n",
     "import matplotlib.pylab as plt\n",
     "import pickle\n",
@@ -25,8 +26,8 @@
     "plt.rcParams['font.sans-serif']='Arial'\n",
     "plt.rcParams['pdf.fonttype']=42\n",
     "# sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap/\"))\n",
-    "import PyComplexHeatmap\n",
-    "from PyComplexHeatmap import *"
+    "from PyComplexHeatmap import *\n",
+    "use_pch_style() # or plt.style.use('default') to restore default style"
    ]
   },
   {

docs/build/doctrees/nbsphinx/notebooks/oncoPrint2.ipynb

@@ -18,6 +18,7 @@
     "import os,sys\n",
     "# sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap/\"))\n",
     "from PyComplexHeatmap import *\n",
+    "use_pch_style() # or plt.style.use('default') to restore default style\n",
     "import pandas as pd\n",
     "import random"
    ]

docs/build/doctrees/nbsphinx/notebooks/single_cell_methylation.ipynb

@@ -34,6 +34,7 @@
     "plt.rcParams['pdf.fonttype']=42\n",
     "# sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap/\"))\n",
     "import PyComplexHeatmap as pch\n",
+    "pch.use_pch_style() # or plt.style.use('default') to restore default style\n",
     "print(pch.__version__)"
    ]
   },

docs/build/html/PyComplexHeatmap.annotations.html

@@ -315,8 +315,8 @@
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_color_dict_legend"><code class="docutils literal notranslate"><span class="pre">plot_color_dict_legend()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_legend_list"><code class="docutils literal notranslate"><span class="pre">plot_legend_list()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_marker_legend"><code class="docutils literal notranslate"><span class="pre">plot_marker_legend()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.set_default_style"><code class="docutils literal notranslate"><span class="pre">set_default_style()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.to_utf8"><code class="docutils literal notranslate"><span class="pre">to_utf8()</span></code></a></li>
+<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.use_pch_style"><code class="docutils literal notranslate"><span class="pre">use_pch_style()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -621,7 +621,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="PyComplexHeatmap.annotations.anno_label">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">PyComplexHeatmap.annotations.</span></span><span class="sig-name descname"><span class="pre">anno_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</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">cmap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colors</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">merge</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">extend</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">frac</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">majority</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_color</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">luminance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</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">legend</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">legend_kws</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">relpos</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">plot_kws</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/PyComplexHeatmap/annotations.html#anno_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#PyComplexHeatmap.annotations.anno_label" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">PyComplexHeatmap.annotations.</span></span><span class="sig-name descname"><span class="pre">anno_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</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">cmap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">colors</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">merge</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">extend</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">frac</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rad</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">majority</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_color</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">luminance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</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">legend</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">legend_kws</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">relpos</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">plot_kws</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/PyComplexHeatmap/annotations.html#anno_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#PyComplexHeatmap.annotations.anno_label" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference internal" href="#PyComplexHeatmap.annotations.AnnotationBase" title="PyComplexHeatmap.annotations.AnnotationBase"><code class="xref py py-class hover docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
 <p>Add label and text annotations. See example on documentatin website:
 <a class="reference external" href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/single_cell_methylation.html">https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/single_cell_methylation.html</a></p>
@@ -630,7 +630,10 @@
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>merge</strong> (<em class="hover">bool</em>) – whether to merge the same clusters into one and label only once.</p></li>
 <li><p><strong>extend</strong> (<em class="hover">bool</em>) – whether to distribute all the labels extend to the all axis, figure or ax or False.</p></li>
-<li><p><strong>frac</strong> (<em class="hover">float</em>) – fraction of the armA and armB.</p></li>
+<li><p><strong>frac</strong> (<em class="hover">float</em>) – fraction of the armA and armB relative to length of connection label, will be passed to
+connectionstyle: f”arc,angleA={angleA},angleB={angleB},armA={arm_height},armB={arm_height},rad={self.rad}”,
+frac will be used to calculate arm_height: arm_height = arrow_height * self.frac</p></li>
+<li><p><strong>rad</strong> (<em class="hover">int</em>) – rad of the connection arrow.</p></li>
 <li><p><strong>majority</strong> (<em class="hover">bool</em>) – If there are multiple group for one label, whether to annotate the label in the largest group. [True]</p></li>
 <li><p><strong>adjust_color</strong> (<em class="hover">bool</em>) – When the luminance of the color is too high, use black color replace the original color. [True]</p></li>
 <li><p><strong>luminance</strong> (<em class="hover">float</em>) – luminance values [0-1], used together with adjust_color, when the calculated luminance &gt; luminance,
@@ -641,10 +644,20 @@
 </dd>
 </dl>
 </p></li>
-<li><p><strong>plot_kws</strong> (<em class="hover">dict</em>) – passed to plt.annotate, including annotation_clip, arrowprops and matplotlib.text.Text,
+<li><p><strong>plot_kws</strong> (<em class="hover">dict</em>) – <p>passed to plt.annotate, including annotation_clip, arrowprops and matplotlib.text.Text,
 more information about arrowprops could be found in
 matplotlib.patches.FancyArrowPatch. For example, to remove arrow, just set
-arrowprops = dict(visible=False,)</p></li>
+arrowprops = dict(visible=False). See: <a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.annotate.html">https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.annotate.html</a> for more information.
+arrowprops:</p>
+<blockquote>
+<div><dl class="simple">
+<dt>arrowstyle:</dt><dd><p><a class="reference external" href="https://matplotlib.org/stable/gallery/text_labels_and_annotations/fancyarrow_demo.html">https://matplotlib.org/stable/gallery/text_labels_and_annotations/fancyarrow_demo.html</a></p>
+</dd>
+<dt>connectionstyle:</dt><dd><p><a class="reference external" href="https://matplotlib.org/stable/gallery/userdemo/connectionstyle_demo.html">https://matplotlib.org/stable/gallery/userdemo/connectionstyle_demo.html</a></p>
+</dd>
+</dl>
+</div></blockquote>
+</p></li>
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>

docs/build/html/PyComplexHeatmap.clustermap.html

@@ -315,8 +315,8 @@
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_color_dict_legend"><code class="docutils literal notranslate"><span class="pre">plot_color_dict_legend()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_legend_list"><code class="docutils literal notranslate"><span class="pre">plot_legend_list()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_marker_legend"><code class="docutils literal notranslate"><span class="pre">plot_marker_legend()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.set_default_style"><code class="docutils literal notranslate"><span class="pre">set_default_style()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.to_utf8"><code class="docutils literal notranslate"><span class="pre">to_utf8()</span></code></a></li>
+<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.use_pch_style"><code class="docutils literal notranslate"><span class="pre">use_pch_style()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -375,8 +375,10 @@
 <li><p><strong>bottom_annotation</strong> (<em class="hover">class AnnotationBase</em>) – the same as top_annotation.</p></li>
 <li><p><strong>left_annotation</strong> (<em class="hover">class AnnotationBase</em>) – the same as top_annotation.</p></li>
 <li><p><strong>right_annotation</strong> (<em class="hover">class AnnotationBase</em>) – the same as top_annotation.</p></li>
-<li><p><strong>row_cluster</strong> (<em class="hover">bool</em>) – whether to perform cluster on rows/columns.</p></li>
-<li><p><strong>col_cluster</strong> (<em class="hover">bool</em>) – whether to perform cluster on rows/columns.</p></li>
+<li><p><strong>row_cluster</strong> (<em class="hover">bool</em>) – whether to perform cluster on rows/columns.
+Setting it to False will preserve the row order of the input data.</p></li>
+<li><p><strong>col_cluster</strong> (<em class="hover">bool</em>) – whether to perform cluster on rows/columns.
+Setting it to False will preserve the column order of the input data.</p></li>
 <li><p><strong>row_cluster_method</strong> (<em class="hover">str</em>) – cluster method for row/columns linkage, such single, complete, average,weighted,
 centroid, median, ward. see scipy.cluster.hierarchy.linkage or
 (<a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html</a>) for detail.</p></li>
@@ -479,8 +481,8 @@
 <li><p><strong>ylabel_bbox_kws</strong> (<em class="hover">dict</em>) – same as xlabel_bbox_kws</p></li>
 <li><p><strong>rasterized</strong> (<em class="hover">bool</em>) – default is auto, when the number of rows or number of cols &gt; 5000,
 rasterized would be automatically set to True to speed up the plotting.</p></li>
-<li><p><strong>kwargs</strong> (<em class="hover">kws passed to plot_heatmap</em><em>, </em><em class="hover">including vmin</em><em>, </em><em class="hover">vmax</em><em>,</em><em class="hover">center</em><em>,</em><em class="hover">robust</em><em>,</em>) – annot, annot_kws, fmt, mask, linewidths linecolor, na_col, cbar,cbar_kwss
-,xticklabels/yticklabels and so on (see ?PyComplexHeatmap.clustermap.plot_heatmap).
+<li><p><strong>kwargs</strong> (<em class="hover">kws passed to plot_heatmap</em><em>, </em><em class="hover">including vmin</em><em>, </em><em class="hover">vmax</em><em>,</em><em class="hover">center</em><em>,</em><em class="hover">robust</em><em>,</em>) – annot, annot_kws, fmt, mask, linewidths linecolor, na_col, cbar,cbar_kwss,
+xticklabels/yticklabels and so on (see ?PyComplexHeatmap.clustermap.plot_heatmap).
 If annot is True, the values of data will be plotted on the top of heatmap,
 if annot is a dataframe, then the custom values will be plotted on heatmap,
 fmt should be set to None if dtype of annot is str. For documentation of

docs/build/html/PyComplexHeatmap.colors.html

@@ -315,8 +315,8 @@
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_color_dict_legend"><code class="docutils literal notranslate"><span class="pre">plot_color_dict_legend()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_legend_list"><code class="docutils literal notranslate"><span class="pre">plot_legend_list()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.plot_marker_legend"><code class="docutils literal notranslate"><span class="pre">plot_marker_legend()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.set_default_style"><code class="docutils literal notranslate"><span class="pre">set_default_style()</span></code></a></li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.to_utf8"><code class="docutils literal notranslate"><span class="pre">to_utf8()</span></code></a></li>
+<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.utils.html#PyComplexHeatmap.utils.use_pch_style"><code class="docutils literal notranslate"><span class="pre">use_pch_style()</span></code></a></li>
 </ul>
 </li>
 </ul>