Update examples and README

igvteam · Apr 22, 2022 · 3de79e4 · 3de79e4
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/igvteam/juicebox-notebook/main?filepath=examples)   _**Jupyter Notebook**_
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/igvteam/juicebox-notebook/main?urlpath=lab/tree/examples)  _**JupyterLab**_
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/igvteam/juicebox-notebook/main?urlpath=lab/tree/examples/RemoteFiles.ipynb)  _**JupyterLab**_
 
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1oLrDItsMZAEQmrsXa9A7MiiMjar0aagW?usp=sharing)
 

diff --git a/examples/ConfigureResolutionAndNormalization.ipynb b/examples/ConfigureResolutionAndNormalization.ipynb
diff --git a/examples/LocalFilePaths.ipynb b/examples/LocalFilePaths.ipynb
@@ -4,9 +4,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Example of loading a map and track from local files.\n",
+    "## Example of loading a map from a local file.\n",
     "\n",
-    "**Note: To use update the 2 \"url\" fields to local file paths**"
+    "**Jupyter Notebook and Colab only -- will not work with JupyterLab.**\n",
+    "\n",
+    "**Note: To use download the test file below and update \"path\" to the local file absolute path**\n",
+    "\n",
+    "```https://s3.amazonaws.com/igv.org.test/data/hic/HCT-116_Cohesin_Loss.hic```"
    ]
   },
   {
@@ -15,14 +19,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pip install juicebox-notebook"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Load a map and track in the intial config"
+    "pip install juicebox-notebook\n"
    ]
   },
   {
@@ -42,63 +39,12 @@
     "b = juicebox_notebook.Browser(\n",
     "    {\n",
     "        \"name\": \"GM12878\",\n",
-    "        \"path\": \"/Volumes/GoogleDrive/Shared drives/IGV/TestData/juicebox/HCT-116_Untreated.hic\",\n",
-    "        \"tracks\": [\n",
-    "            {\n",
-    "                \"path\": \"/Volumes/GoogleDrive/Shared drives/IGV/TestData/juicebox/CTCF_Untreated.bw\",\n",
-    "                \"type\": \"wig\",\n",
-    "                \"name\": \"CTCF\",\n",
-    "                \"color\": \"rgb(22, 129, 198)\"\n",
-    "            }\n",
-    "        ]\n",
+    "        \"path\": \"/your/local/path/HCT-116_Untreated.hic\"\n",
     "    }\n",
-    "\n",
     ")\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "pycharm": {
-     "name": "#%% md\n"
-    }
-   },
-   "source": [
-    "### Load a map and track dynamically"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import juicebox_notebook\n",
-    "\n",
-    "juicebox_notebook.init()\n",
     "\n",
-    "b = juicebox_notebook.Browser({})\n",
-    "\n",
-    "b.load_map({\n",
-    "  \"name\": \"GM12878\",\n",
-    "  \"path\": \"/Volumes/GoogleDrive/Shared drives/IGV/TestData/juicebox/HCT-116_Untreated.hic\"\n",
-    "})\n",
-    "\n",
-    "b.load_track({\n",
-    "  \"path\": \"/Volumes/GoogleDrive/Shared drives/IGV/TestData/juicebox/CTCF_Untreated.bw\",\n",
-    "  \"type\": \"wig\",\n",
-    "  \"name\": \"CTCF\",\n",
-    "  \"color\": \"rgb(22, 129, 198)\"\n",
-    "})\n"
+    "\n"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -122,4 +68,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/examples/RemoteFiles.ipynb b/examples/RemoteFiles.ipynb
@@ -1,5 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "**Install juicebox-notebook**"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -13,6 +24,88 @@
     "pip install juicebox-notebook"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "**Load map and tracks during Browser initialization**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "import juicebox_notebook\n",
+    "\n",
+    "juicebox_notebook.init()\n",
+    "\n",
+    "b = juicebox_notebook.Browser({\n",
+    "                \"url\": \"https://www.encodeproject.org/files/ENCFF718AWL/@@download/ENCFF718AWL.hic\",\n",
+    "                \"name\": \"GM12878\",\n",
+    "                \"locus\": \"ace\",\n",
+    "                \"normalization\": \"VC_SQRT\",\n",
+    "                \"resolution\": \"25000\",\n",
+    "                \"tracks\":     [{\n",
+    "                                  \"url\": \"https://www.encodeproject.org/files/ENCFF000ARJ/@@download/ENCFF000ARJ.bigWig\",\n",
+    "                                  \"name\": \"CTCF\",\n",
+    "                                  \"color\": \"#ff8802\"\n",
+    "                              }]\n",
+    "            })\n"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "**Load map and tracks dynamically**"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "import juicebox_notebook\n",
+    "\n",
+    "juicebox_notebook.init()\n",
+    "\n",
+    "b = juicebox_notebook.Browser({})\n",
+    "\n",
+    "b.load_map({\n",
+    "    \"url\": \"https://www.encodeproject.org/files/ENCFF718AWL/@@download/ENCFF718AWL.hic\",\n",
+    "    \"name\": \"GM12878\"\n",
+    "})\n",
+    "\n",
+    "b.load_track_list(\n",
+    "    [{\n",
+    "        \"url\": \"https://www.encodeproject.org/files/ENCFF000ARJ/@@download/ENCFF000ARJ.bigWig\",\n",
+    "        \"name\": \"CTCF\",\n",
+    "        \"color\": \"#ff8802\"\n",
+    "    }]\n",
+    ")\n",
+    "\n",
+    "\n"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -29,24 +122,56 @@
     "\n",
     "b = juicebox_notebook.Browser({})\n",
     "\n",
-    "b.load_map(\n",
-    "    {\n",
-    "         \"url\": \"https://www.encodeproject.org/files/ENCFF179HVU/@@download/ENCFF179HVU.hic\"\n",
-    "    }\n",
+    "b.load_map({\n",
+    "    \"url\": \"https://www.encodeproject.org/files/ENCFF718AWL/@@download/ENCFF718AWL.hic\",\n",
+    "    \"name\": \"GM12878\"\n",
+    "})\n",
+    "\n",
+    "b.load_track_list(\n",
+    "    [{\n",
+    "        \"url\": \"https://www.encodeproject.org/files/ENCFF000ARJ/@@download/ENCFF000ARJ.bigWig\",\n",
+    "        \"name\": \"CTCF\",\n",
+    "        \"color\": \"#ff8802\"\n",
+    "    }]\n",
     ")\n",
     "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Load map and tracks dynamically**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import juicebox_notebook\n",
+    "\n",
+    "juicebox_notebook.init()\n",
+    "\n",
+    "b = juicebox_notebook.Browser({})\n",
+    "\n",
+    "b.load_map({\n",
+    "    \"url\": \"https://www.encodeproject.org/files/ENCFF718AWL/@@download/ENCFF718AWL.hic\",\n",
+    "    \"name\": \"GM12878\"\n",
+    "})\n",
+    "\n",
     "b.load_track_list(\n",
-    "    [\n",
-    "        {\n",
-    "            \"url\": \"https://www.encodeproject.org/files/ENCFF000ARJ/@@download/ENCFF000ARJ.bigWig\",\n",
-    "            \"name\": \"CTCF\",\n",
-    "            \"color\": \"#ff8802\"\n",
-    "        },\n",
-    "        {\n",
-    "            \"url\": \"https://hicfiles.s3.amazonaws.com/hiseq/nhek/in-situ/combined_blocks.txt\",\n",
-    "            \"name\": \"Rao & Huntley et al. | Cell 2014 | NHEK combined domains\"\n",
-    "        }\n",
-    "    ]\n",
+    "    [{\n",
+    "        \"url\": \"https://www.encodeproject.org/files/ENCFF000ARJ/@@download/ENCFF000ARJ.bigWig\",\n",
+    "        \"name\": \"CTCF\",\n",
+    "        \"color\": \"#ff8802\"\n",
+    "    }]\n",
     ")\n",
     "\n",
     "\n"

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(name='juicebox-notebook',
                  packages=['juicebox_notebook'],
-                 version='0.2.0',
+                 version='0.2.1',
                  description='Package for embedding the juicebox.js hic visualization in IPython notebooks',
                  long_description=long_description,
                  long_description_content_type="text/markdown",