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update readme and docs
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‎README.md‎

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@@ -70,13 +70,13 @@ Click picture to view the source code
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<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
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<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Modifying-xlabel-and-ylabel-using-xlabel_kws-and-ylabel_kws">
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<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/anno_img_example.html#Visualizing-motif-enrichment-results-using-anno_img">
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<img src="docs/images/gallery11.png" title="Modify labels" align="center" width="250px">
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</a>
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</td>
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<td style="width:33%; background-color:white;text-align:center; vertical-align:middle">
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<a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/composite_heatmaps.html#Composite-two-heatmaps-horizontally-for-mouse-DNA-methylation-array-dataset">
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<img src="docs/images/gallery3.jpg" title="Combine two heatmap horizontally" align="center" width="250px">
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<img src="docs/images/gallery3.png" title="Combine two heatmap horizontally" align="center" width="250px">
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</tr>

‎docs/build/doctrees/environment.pickle‎

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

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@@ -32,7 +32,7 @@
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"mpl.rcParams['figure.dpi'] = 80\n",
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"mpl.rcParams['savefig.dpi']=300\n",
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"import pickle\n",
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"# sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap\"))\n",
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"sys.path.append(os.path.expanduser(\"~/Projects/Github/PyComplexHeatmap\"))\n",
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"from PyComplexHeatmap import (\n",
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" ClusterMapPlotter,DotClustermapPlotter,HeatmapAnnotation,anno_simple,anno_scatterplot,anno_lineplot,anno_barplot,\n",
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" anno_label,anno_boxplot,anno_img,\n",
@@ -701,25 +701,6 @@
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"execution_count": 6,
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"id": "70924974-bcda-4a49-9552-01cf38312a52",
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"metadata": {},
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"outputs": [],
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"source": [
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"# # download image to local\n",
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"# import requests\n",
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"# img_dir='images'\n",
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"# if not os.path.exists(img_dir):\n",
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"# os.mkdir(img_dir)\n",
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"# for url in df_row.Logo.tolist():\n",
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"# img_data = requests.get(url).content\n",
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"# file=os.path.basename(url)\n",
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"# with open(os.path.join(img_dir,file), 'wb') as handler:\n",
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"# handler.write(img_data)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "3ffb2fa2-b1b6-4211-999f-c6978bbdf15a",
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"metadata": {},
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"outputs": [
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{
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"data": {
@@ -767,7 +748,7 @@
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" <td>0.767527</td>\n",
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" <td>-0.149461</td>\n",
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" <td>ASC|Nfia</td>\n",
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" <td>images/jaspar__MA0670.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Tcf4</th>\n",
@@ -776,7 +757,7 @@
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" <td>0.508175</td>\n",
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" <td>-0.282496</td>\n",
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" <td>CGE-Vip|Tcf4</td>\n",
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" <td>images/tfdimers__MD00119.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Erg</th>\n",
@@ -785,7 +766,7 @@
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" <td>0.857981</td>\n",
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" <td>-0.114057</td>\n",
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" <td>EC|Erg</td>\n",
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" <td>images/metacluster_135.7.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Fli1</th>\n",
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" <td>0.747177</td>\n",
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" <td>-0.171242</td>\n",
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" <td>EC|Fli1</td>\n",
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" <td>images/metacluster_135.7.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Zbtb43</th>\n",
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" <td>0.784200</td>\n",
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" <td>-0.144034</td>\n",
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" <td>Exc|Zbtb43</td>\n",
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" <td>images/metacluster_131.8.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Mef2c</th>\n",
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" <td>0.680693</td>\n",
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" <td>-0.177612</td>\n",
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" <td>IT-L6|Mef2c</td>\n",
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" <td>images/transfac_pro__M04846.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Spi1</th>\n",
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" <td>0.736412</td>\n",
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" <td>-0.185941</td>\n",
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" <td>MGC|Spi1</td>\n",
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" <td>images/metacluster_167.5.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Hdx</th>\n",
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" <td>0.852639</td>\n",
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" <td>-0.120034</td>\n",
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" <td>MGC|Hdx</td>\n",
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" <td>images/tfdimers__MD00488.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Bach1</th>\n",
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" <td>0.855795</td>\n",
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" <td>-0.100834</td>\n",
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" <td>MGE-Pvalb|Bach1</td>\n",
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" <td>images/jaspar__MA1633.2.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Sox10</th>\n",
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" <td>0.280051</td>\n",
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" <td>-0.354296</td>\n",
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" <td>ODC|Sox10</td>\n",
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" <td>images/metacluster_4.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Sox8</th>\n",
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" <td>0.361547</td>\n",
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" <td>-0.215307</td>\n",
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" <td>ODC|Sox8</td>\n",
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" <td>images/metacluster_4.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Emx1</th>\n",
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" <td>0.655946</td>\n",
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" <td>-0.114102</td>\n",
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" <td>P|Emx1</td>\n",
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" <td>images/metacluster_164.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Lhx2</th>\n",
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" <td>0.623909</td>\n",
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" <td>-0.101292</td>\n",
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" <td>P|Lhx2</td>\n",
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" <td>images/metacluster_164.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Lhx3</th>\n",
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" <td>0.550733</td>\n",
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" <td>-0.109488</td>\n",
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" <td>P|Lhx3</td>\n",
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" <td>images/metacluster_9.26.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Pou5f1</th>\n",
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" <td>0.800837</td>\n",
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" <td>-0.124454</td>\n",
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" <td>P|Pou5f1</td>\n",
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" <td>images/taipale_cyt_meth__POU5F1_NYTAATTATGCGNR...</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Barhl1</th>\n",
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" <td>0.469806</td>\n",
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" <td>-0.116628</td>\n",
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" <td>P|Barhl1</td>\n",
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" <td>images/metacluster_124.2.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Emx2</th>\n",
@@ -911,7 +892,7 @@
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" <td>0.522485</td>\n",
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" <td>-0.105113</td>\n",
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" <td>P|Emx2</td>\n",
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" <td>images/metacluster_164.1.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Hnf1b</th>\n",
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" <td>0.793915</td>\n",
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" <td>-0.115062</td>\n",
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" <td>PC|Hnf1b</td>\n",
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" <td>images/tfdimers__MD00345.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Ebf4</th>\n",
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" <td>0.797483</td>\n",
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" <td>-0.125697</td>\n",
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" <td>PC|Ebf4</td>\n",
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" <td>images/metacluster_172.20.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Ebf1</th>\n",
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" <td>0.821295</td>\n",
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" <td>-0.125705</td>\n",
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" <td>PC|Ebf1</td>\n",
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" <td>images/metacluster_172.20.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Ovol2</th>\n",
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" <td>0.775894</td>\n",
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" <td>-0.119117</td>\n",
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" <td>PC|Ovol2</td>\n",
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" <td>images/tfdimers__MD00481.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>Ikzf2</th>\n",
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" <td>0.830263</td>\n",
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" <td>-0.130275</td>\n",
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" <td>PC|Ikzf2</td>\n",
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" <td>images/tfdimers__MD00008.png</td>\n",
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" <td>https://motifcollections.aertslab.org/v10nr_cl...</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"\n",
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" Logo \n",
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"Gene \n",
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"Nfia images/jaspar__MA0670.1.png \n",
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"Tcf4 images/tfdimers__MD00119.png \n",
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"Erg images/metacluster_135.7.png \n",
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"Fli1 images/metacluster_135.7.png \n",
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"Zbtb43 images/metacluster_131.8.png \n",
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"Mef2c images/transfac_pro__M04846.png \n",
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"Spi1 images/metacluster_167.5.png \n",
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"Hdx images/tfdimers__MD00488.png \n",
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"Bach1 images/jaspar__MA1633.2.png \n",
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"Sox10 images/metacluster_4.1.png \n",
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"Sox8 images/metacluster_4.1.png \n",
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"Emx1 images/metacluster_164.1.png \n",
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"Lhx2 images/metacluster_164.1.png \n",
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"Lhx3 images/metacluster_9.26.png \n",
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"Pou5f1 images/taipale_cyt_meth__POU5F1_NYTAATTATGCGNR... \n",
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"Barhl1 images/metacluster_124.2.png \n",
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"Emx2 images/metacluster_164.1.png \n",
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"Hnf1b images/tfdimers__MD00345.png \n",
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"Ebf4 images/metacluster_172.20.png \n",
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"Ebf1 images/metacluster_172.20.png \n",
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"Ovol2 images/tfdimers__MD00481.png \n",
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"Ikzf2 images/tfdimers__MD00008.png "
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"Nfia https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Tcf4 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Erg https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Fli1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Zbtb43 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Mef2c https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Spi1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Hdx https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Bach1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Sox10 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Sox8 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Emx1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Lhx2 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Lhx3 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Pou5f1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Barhl1 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Emx2 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Hnf1b https://motifcollections.aertslab.org/v10nr_cl... \n",
992+
"Ebf4 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Ebf1 https://motifcollections.aertslab.org/v10nr_cl... \n",
994+
"Ovol2 https://motifcollections.aertslab.org/v10nr_cl... \n",
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"Ikzf2 https://motifcollections.aertslab.org/v10nr_cl... "
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]
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},
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"execution_count": 7,
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"img_dir='images'\n",
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"df_row.Logo=df_row.Logo.apply(lambda x:os.path.join(img_dir,os.path.basename(x)))\n",
1004+
"# # Images could be a url or file path, for example: download image to local\n",
1005+
"# import requests\n",
1006+
"# img_dir='images'\n",
1007+
"# if not os.path.exists(img_dir):\n",
1008+
"# os.mkdir(img_dir)\n",
1009+
"# for url in df_row.Logo.tolist():\n",
1010+
"# img_data = requests.get(url).content\n",
1011+
"# file=os.path.basename(url)\n",
1012+
"# with open(os.path.join(img_dir,file), 'wb') as handler:\n",
1013+
"# handler.write(img_data)\n",
1014+
"\n",
1015+
"# img_dir='images'\n",
1016+
"# df_row.Logo=df_row.Logo.apply(lambda x:os.path.join(img_dir,os.path.basename(x)))\n",
10251017
"df_row"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"execution_count": 7,
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"id": "8683f2d4-cea6-445f-ae32-cbfdb835b2ee",
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"metadata": {
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"tags": []
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "17c5d0c9-c934-4fa5-ae24-1a5110e7f0a9",
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"metadata": {
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"tags": []

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