update docs

DingWB · Apr 6, 2024 · 41794a6 · 41794a6
1 parent c4c5a11
commit 41794a6
Show file tree

Hide file tree

Showing 58 changed files with 961 additions and 920 deletions.
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/nbsphinx/notebooks/advanced_usage.ipynb b/docs/build/doctrees/nbsphinx/notebooks/advanced_usage.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks/dotHeatmap.ipynb b/docs/build/doctrees/nbsphinx/notebooks/dotHeatmap.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_10_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_10_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_12_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_12_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_14_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_14_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_16_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_16_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_18_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_18_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_19_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_19_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_23_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_23_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_25_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_25_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_27_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_27_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_28_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_28_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_30_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_30_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_32_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_32_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_33_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_33_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_36_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_36_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_44_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_44_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_46_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_46_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_47_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_47_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_49_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_49_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_51_0.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_51_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_5_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_5_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_7_1.png b/docs/build/doctrees/nbsphinx/notebooks_advanced_usage_7_1.png
diff --git a/...es/nbsphinx/notebooks_dotHeatmap_14_2.png → ...es/nbsphinx/notebooks_dotHeatmap_14_3.png b/...es/nbsphinx/notebooks_dotHeatmap_14_2.png → ...es/nbsphinx/notebooks_dotHeatmap_14_3.png
diff --git a/docs/build/doctrees/notebooks/advanced_usage.doctree b/docs/build/doctrees/notebooks/advanced_usage.doctree
diff --git a/docs/build/doctrees/notebooks/dotHeatmap.doctree b/docs/build/doctrees/notebooks/dotHeatmap.doctree
diff --git a/docs/build/html/_images/notebooks_advanced_usage_10_1.png b/docs/build/html/_images/notebooks_advanced_usage_10_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_12_1.png b/docs/build/html/_images/notebooks_advanced_usage_12_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_14_1.png b/docs/build/html/_images/notebooks_advanced_usage_14_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_16_1.png b/docs/build/html/_images/notebooks_advanced_usage_16_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_18_1.png b/docs/build/html/_images/notebooks_advanced_usage_18_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_19_1.png b/docs/build/html/_images/notebooks_advanced_usage_19_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_23_0.png b/docs/build/html/_images/notebooks_advanced_usage_23_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_25_0.png b/docs/build/html/_images/notebooks_advanced_usage_25_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_27_0.png b/docs/build/html/_images/notebooks_advanced_usage_27_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_28_0.png b/docs/build/html/_images/notebooks_advanced_usage_28_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_30_0.png b/docs/build/html/_images/notebooks_advanced_usage_30_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_32_1.png b/docs/build/html/_images/notebooks_advanced_usage_32_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_33_0.png b/docs/build/html/_images/notebooks_advanced_usage_33_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_36_1.png b/docs/build/html/_images/notebooks_advanced_usage_36_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_44_0.png b/docs/build/html/_images/notebooks_advanced_usage_44_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_46_0.png b/docs/build/html/_images/notebooks_advanced_usage_46_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_47_0.png b/docs/build/html/_images/notebooks_advanced_usage_47_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_49_0.png b/docs/build/html/_images/notebooks_advanced_usage_49_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_51_0.png b/docs/build/html/_images/notebooks_advanced_usage_51_0.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_5_1.png b/docs/build/html/_images/notebooks_advanced_usage_5_1.png
diff --git a/docs/build/html/_images/notebooks_advanced_usage_7_1.png b/docs/build/html/_images/notebooks_advanced_usage_7_1.png
diff --git a/...tml/_images/notebooks_dotHeatmap_14_2.png → ...tml/_images/notebooks_dotHeatmap_14_3.png b/...tml/_images/notebooks_dotHeatmap_14_2.png → ...tml/_images/notebooks_dotHeatmap_14_3.png
diff --git a/docs/build/html/_sources/notebooks/advanced_usage.ipynb.txt b/docs/build/html/_sources/notebooks/advanced_usage.ipynb.txt
diff --git a/docs/build/html/_sources/notebooks/dotHeatmap.ipynb.txt b/docs/build/html/_sources/notebooks/dotHeatmap.ipynb.txt
diff --git a/docs/build/html/notebooks/advanced_usage.html b/docs/build/html/notebooks/advanced_usage.html
diff --git a/docs/build/html/notebooks/advanced_usage.ipynb b/docs/build/html/notebooks/advanced_usage.ipynb
diff --git a/docs/build/html/notebooks/dotHeatmap.html b/docs/build/html/notebooks/dotHeatmap.html
@@ -356,7 +356,7 @@
 <span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;font.family&#39;</span><span class="p">]</span><span class="o">=</span><span class="s1">&#39;sans serif&#39;</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;font.sans-serif&#39;</span><span class="p">]</span><span class="o">=</span><span class="s1">&#39;Arial&#39;</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;pdf.fonttype&#39;</span><span class="p">]</span><span class="o">=</span><span class="mi">42</span>
-<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="s2">&quot;~/Projects/Github/PyComplexHeatmap/&quot;</span><span class="p">))</span>
+<span class="c1"># sys.path.append(os.path.expanduser(&quot;~/Projects/Github/PyComplexHeatmap/&quot;))</span>
 <span class="kn">import</span> <span class="nn">PyComplexHeatmap</span>
 <span class="kn">from</span> <span class="nn">PyComplexHeatmap</span> <span class="kn">import</span> <span class="o">*</span>
 </pre></div>
@@ -834,24 +834,31 @@ <h1>Add parameter <code class="docutils literal notranslate"><span class="pre">h
 Plotting matrix..
 Inferred max_s (max size of scatter point) is: 132.808800071564
 Collecting legends..
-Plotting legends..
-Estimated legend width: 28.22361111111111 mm
 </pre></div></div>
 </div>
 <div class="nboutput docutils container">
 <div class="prompt empty docutils container">
 </div>
 <div class="output_area stderr docutils container">
 <div class="highlight"><pre>
-/Users/wding/Projects/Github/PyComplexHeatmap/PyComplexHeatmap/dotHeatmap.py:189: UserWarning: No data for colormapping provided via &#39;c&#39;. Parameters &#39;cmap&#39;, &#39;norm&#39; will be ignored
+/Users/wding/Software/miniconda3/envs/wding/lib/python3.8/site-packages/PyComplexHeatmap/dotHeatmap.py:189: UserWarning: No data for colormapping provided via &#39;c&#39;. Parameters &#39;cmap&#39;, &#39;norm&#39; will be ignored
   ax.scatter(
 </pre></div></div>
 </div>
+<div class="nboutput docutils container">
+<div class="prompt empty docutils container">
+</div>
+<div class="output_area docutils container">
+<div class="highlight"><pre>
+Plotting legends..
+Estimated legend width: 28.22361111111111 mm
+</pre></div></div>
+</div>
 <div class="nboutput nblast docutils container">
 <div class="prompt empty docutils container">
 </div>
 <div class="output_area docutils container">
-<img alt="../_images/notebooks_dotHeatmap_14_2.png" src="../_images/notebooks_dotHeatmap_14_2.png" />
+<img alt="../_images/notebooks_dotHeatmap_14_3.png" src="../_images/notebooks_dotHeatmap_14_3.png" />
 </div>
 </div>
 </section>
@@ -1054,7 +1061,7 @@ <h1>Plot clustermap using seaborn brain networks dataset<a class="headerlink" hr
 <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="headerlink" href="#Visualize-up-to-five-dimension-data-using-DotClustermapPlotter" title="Permalink to this heading">¶</a></h1>
 <p>Plot enrichment analysis result using example dataset with samples annotations</p>
 <div class="nbinput nblast docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[14]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span><span class="o">=</span><span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;../data/kycg_result.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
@@ -1079,15 +1086,15 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[15]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
 </pre></div>
 </div>
 </div>
 <div class="nboutput nblast docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[15]:
 </pre></div>
 </div>
 <div class="output_area rendered_html docutils container">
@@ -1186,15 +1193,15 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[16]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;-log10(Pval)&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
 </pre></div>
 </div>
 </div>
 <div class="nboutput nblast docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[16]:
 </pre></div>
 </div>
 <div class="output_area docutils container">
@@ -1211,7 +1218,7 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </pre></div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[17]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">CpGType</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
@@ -1229,15 +1236,15 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </pre></div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[18]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">df_col</span>
 </pre></div>
 </div>
 </div>
 <div class="nboutput nblast docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[18]:
 </pre></div>
 </div>
 <div class="output_area rendered_html docutils container">
@@ -1294,15 +1301,15 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[19]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">df_row</span>
 </pre></div>
 </div>
 </div>
 <div class="nboutput nblast docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[19]:
 </pre></div>
 </div>
 <div class="output_area rendered_html docutils container">
@@ -1413,7 +1420,7 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[20]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">row_ha</span> <span class="o">=</span> <span class="n">HeatmapAnnotation</span><span class="p">(</span>
@@ -1467,7 +1474,7 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[21]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">3.5</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
@@ -1533,7 +1540,7 @@ <h1>Visualize up to five dimension data using DotClustermapPlotter<a class="head
 </pre></div></div>
 </div>
 <div class="nbinput docutils container">
-<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[23]:
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">3.5</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>

diff --git a/docs/build/html/notebooks/dotHeatmap.ipynb b/docs/build/html/notebooks/dotHeatmap.ipynb
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
diff --git a/notebooks/advanced_usage.ipynb b/notebooks/advanced_usage.ipynb
diff --git a/notebooks/dotHeatmap.ipynb b/notebooks/dotHeatmap.ipynb