fix bug for anno_img

DingWB · Apr 19, 2024 · 8c38982 · 8c38982
1 parent ea925cb
commit 8c38982
Show file tree

Hide file tree

Showing 140 changed files with 10,561 additions and 4,848 deletions.
diff --git a/data/anno_img_example.pickle b/data/anno_img_example.pickle
diff --git a/data/enrichment_analysis_dotHeatmap.pickle b/data/enrichment_analysis_dotHeatmap.pickle
diff --git a/docs/build/doctrees/PyComplexHeatmap.annotations.doctree b/docs/build/doctrees/PyComplexHeatmap.annotations.doctree
diff --git a/docs/build/doctrees/PyComplexHeatmap.doctree b/docs/build/doctrees/PyComplexHeatmap.doctree
diff --git a/docs/build/doctrees/PyComplexHeatmap.example.doctree b/docs/build/doctrees/PyComplexHeatmap.example.doctree
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/anno_img_example.ipynb b/docs/build/doctrees/nbsphinx/notebooks/anno_img_example.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks/cpg_modules.ipynb b/docs/build/doctrees/nbsphinx/notebooks/cpg_modules.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks/dev.ipynb b/docs/build/doctrees/nbsphinx/notebooks/dev.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks/gene_enrichment_analysis.ipynb b/docs/build/doctrees/nbsphinx/notebooks/gene_enrichment_analysis.ipynb
diff --git a/docs/build/doctrees/nbsphinx/notebooks/test.ipynb b/docs/build/doctrees/nbsphinx/notebooks/test.ipynb
@@ -0,0 +1,74 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "5abd163d-47c1-4419-ae06-c6be2c69a624",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1.7.2.dev0+g8abf70a.d20240415\n"
+     ]
+    }
+   ],
+   "source": [
+    "import os,sys\n",
+    "%matplotlib inline\n",
+    "import matplotlib.pylab as plt\n",
+    "import pickle\n",
+    "plt.rcParams['figure.dpi'] = 100\n",
+    "plt.rcParams['savefig.dpi']=300\n",
+    "sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap\"))\n",
+    "import PyComplexHeatmap\n",
+    "print(PyComplexHeatmap.__version__)\n",
+    "from PyComplexHeatmap import *"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "eed2f250-92b2-434c-b268-22b4be27d4f6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#set font to Arial using the following code\n",
+    "plt.rcParams['font.family']='sans serif'\n",
+    "plt.rcParams['font.sans-serif']='Arial'\n",
+    "# set pdf.fonttype to 42\n",
+    "plt.rcParams['pdf.fonttype']=42"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "548e870f-91fc-4f63-91d8-96f8822cbf36",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "wding",
+   "language": "python",
+   "name": "wding"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/build/doctrees/nbsphinx/notebooks/test_add_anno_img.ipynb b/docs/build/doctrees/nbsphinx/notebooks/test_add_anno_img.ipynb
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_anno_img_example_10_1.png b/docs/build/doctrees/nbsphinx/notebooks_anno_img_example_10_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_anno_img_example_11_1.png b/docs/build/doctrees/nbsphinx/notebooks_anno_img_example_11_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_12_1.png b/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_12_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_15_0.png b/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_15_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_16_0.png b/docs/build/doctrees/nbsphinx/notebooks_cpg_modules_16_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_10_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_10_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_11_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_11_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_12_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_12_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_15_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_15_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_16_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_16_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_17_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_17_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_18_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_18_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_20_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_20_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_21_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_21_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_23_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_23_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_26_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_26_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_27_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_27_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_28_1.png b/docs/build/doctrees/nbsphinx/notebooks_dev_28_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_dev_4_0.png b/docs/build/doctrees/nbsphinx/notebooks_dev_4_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_gene_enrichment_analysis_16_1.png b/docs/build/doctrees/nbsphinx/notebooks_gene_enrichment_analysis_16_1.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_3_0.png b/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_3_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_4_0.png b/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_4_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_5_0.png b/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_5_0.png
diff --git a/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_7_1.png b/docs/build/doctrees/nbsphinx/notebooks_test_add_anno_img_7_1.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/anno_img_example.doctree b/docs/build/doctrees/notebooks/anno_img_example.doctree
diff --git a/docs/build/doctrees/notebooks/cpg_modules.doctree b/docs/build/doctrees/notebooks/cpg_modules.doctree
diff --git a/docs/build/doctrees/notebooks/dev.doctree b/docs/build/doctrees/notebooks/dev.doctree
diff --git a/docs/build/doctrees/notebooks/gene_enrichment_analysis.doctree b/docs/build/doctrees/notebooks/gene_enrichment_analysis.doctree
diff --git a/docs/build/doctrees/notebooks/kwargs.doctree b/docs/build/doctrees/notebooks/kwargs.doctree
diff --git a/docs/build/doctrees/notebooks/test.doctree b/docs/build/doctrees/notebooks/test.doctree
diff --git a/docs/build/doctrees/notebooks/test_add_anno_img.doctree b/docs/build/doctrees/notebooks/test_add_anno_img.doctree
diff --git a/docs/build/html/PyComplexHeatmap.annotations.html b/docs/build/html/PyComplexHeatmap.annotations.html
diff --git a/docs/build/html/PyComplexHeatmap.clustermap.html b/docs/build/html/PyComplexHeatmap.clustermap.html
@@ -162,7 +162,13 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="gallery.html">Gallery</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dev.html">For Developers</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html">1. Understand the layout:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html">Understand the layout:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#Test-dendrogram">Test dendrogram</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#anno_label">anno_label</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#anno_img">anno_img</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/dev.html#extent">extent</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="modules.html">PyComplexHeatmap</a><ul class="current">
@@ -177,6 +183,7 @@
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_axes_kws"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_axes_kws()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_label"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_label()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_legend"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_legend()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_orientation"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_orientation()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.update_plot_kws"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.update_plot_kws()</span></code></a></li>
 </ul>
 </li>
@@ -198,13 +205,13 @@
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img"><code class="docutils literal notranslate"><span class="pre">anno_img</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img.plot"><code class="docutils literal notranslate"><span class="pre">anno_img.plot()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img.read_img"><code class="docutils literal notranslate"><span class="pre">anno_img.read_img()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label"><code class="docutils literal notranslate"><span class="pre">anno_label</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.get_ticklabel_width"><code class="docutils literal notranslate"><span class="pre">anno_label.get_ticklabel_width()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.plot"><code class="docutils literal notranslate"><span class="pre">anno_label.plot()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.set_plot_kws"><code class="docutils literal notranslate"><span class="pre">anno_label.set_plot_kws()</span></code></a></li>
-<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.set_side"><code class="docutils literal notranslate"><span class="pre">anno_label.set_side()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_lineplot"><code class="docutils literal notranslate"><span class="pre">anno_lineplot</span></code></a><ul>
@@ -278,12 +285,6 @@
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.dotHeatmap.html#PyComplexHeatmap.dotHeatmap.scale"><code class="docutils literal notranslate"><span class="pre">scale()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l4"><a class="reference internal" href="PyComplexHeatmap.example.html">PyComplexHeatmap.example module</a><ul>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.clustermap_example0"><code class="docutils literal notranslate"><span class="pre">clustermap_example0()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.clustermap_example1"><code class="docutils literal notranslate"><span class="pre">clustermap_example1()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.get_kycg_example_data"><code class="docutils literal notranslate"><span class="pre">get_kycg_example_data()</span></code></a></li>
-</ul>
-</li>
 <li class="toctree-l4"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html">PyComplexHeatmap.oncoPrint module</a><ul>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html#PyComplexHeatmap.oncoPrint.oncoPrintPlotter"><code class="docutils literal notranslate"><span class="pre">oncoPrintPlotter</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html#PyComplexHeatmap.oncoPrint.oncoPrintPlotter.add_default_annotations"><code class="docutils literal notranslate"><span class="pre">oncoPrintPlotter.add_default_annotations()</span></code></a></li>

diff --git a/docs/build/html/PyComplexHeatmap.colors.html b/docs/build/html/PyComplexHeatmap.colors.html
@@ -162,7 +162,13 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="gallery.html">Gallery</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dev.html">For Developers</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html">1. Understand the layout:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html">Understand the layout:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#Test-dendrogram">Test dendrogram</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#anno_label">anno_label</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/dev.html#anno_img">anno_img</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/dev.html#extent">extent</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="modules.html">PyComplexHeatmap</a><ul class="current">
@@ -177,6 +183,7 @@
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_axes_kws"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_axes_kws()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_label"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_label()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_legend"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_legend()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.set_orientation"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.set_orientation()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.update_plot_kws"><code class="docutils literal notranslate"><span class="pre">AnnotationBase.update_plot_kws()</span></code></a></li>
 </ul>
 </li>
@@ -198,13 +205,13 @@
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img"><code class="docutils literal notranslate"><span class="pre">anno_img</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img.plot"><code class="docutils literal notranslate"><span class="pre">anno_img.plot()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_img.read_img"><code class="docutils literal notranslate"><span class="pre">anno_img.read_img()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label"><code class="docutils literal notranslate"><span class="pre">anno_label</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.get_ticklabel_width"><code class="docutils literal notranslate"><span class="pre">anno_label.get_ticklabel_width()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.plot"><code class="docutils literal notranslate"><span class="pre">anno_label.plot()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.set_plot_kws"><code class="docutils literal notranslate"><span class="pre">anno_label.set_plot_kws()</span></code></a></li>
-<li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.set_side"><code class="docutils literal notranslate"><span class="pre">anno_label.set_side()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_lineplot"><code class="docutils literal notranslate"><span class="pre">anno_lineplot</span></code></a><ul>
@@ -278,12 +285,6 @@
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.dotHeatmap.html#PyComplexHeatmap.dotHeatmap.scale"><code class="docutils literal notranslate"><span class="pre">scale()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l4"><a class="reference internal" href="PyComplexHeatmap.example.html">PyComplexHeatmap.example module</a><ul>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.clustermap_example0"><code class="docutils literal notranslate"><span class="pre">clustermap_example0()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.clustermap_example1"><code class="docutils literal notranslate"><span class="pre">clustermap_example1()</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.example.html#PyComplexHeatmap.example.get_kycg_example_data"><code class="docutils literal notranslate"><span class="pre">get_kycg_example_data()</span></code></a></li>
-</ul>
-</li>
 <li class="toctree-l4"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html">PyComplexHeatmap.oncoPrint module</a><ul>
 <li class="toctree-l5"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html#PyComplexHeatmap.oncoPrint.oncoPrintPlotter"><code class="docutils literal notranslate"><span class="pre">oncoPrintPlotter</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="PyComplexHeatmap.oncoPrint.html#PyComplexHeatmap.oncoPrint.oncoPrintPlotter.add_default_annotations"><code class="docutils literal notranslate"><span class="pre">oncoPrintPlotter.add_default_annotations()</span></code></a></li>