Getting_Started.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Getting started ###\n",
    "This notebook provides a few examples of working with the IDR data.\n",
    "Functions can be found in [idr-py](https://github.com/IDR/idr-py/). Feel free\n",
    "to copy notebooks into the scratch space and edit as necessary.\n",
    "**All** changes should be considered temporary. Download a copy of\n",
    "notebooks and results when your session is complete."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from IPython.display import display, Image\n",
    "from IPython import get_ipython\n",
    "from idr import connection\n",
    "from idr import images_by_phenotype, attributes_by_attributes\n",
    "from idr import simple_colocalisation\n",
    "get_ipython().run_line_magic('matplotlib', 'inline')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "No handlers could be found for logger \"omero.gateway\"\n"
     ]
    }
   ],
   "source": [
    "conn = connection()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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     "metadata": {},
     "output_type": "display_data"
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     "output_type": "display_data"
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
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      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/jpeg": "/9j/4AAQSkZJRgABAgAAAQABAAD/2wBDAAUDBAQEAwUEBAQFBQUGBwwIBwcHBw8KCwkMEQ8SEhEP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\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "images = images_by_phenotype(conn, \"CMPO_0000077\")\n",
    "display(*tuple([Image(img.getThumbnail()) for img in images[100:2500:500]]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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ldGu2a6idVbHSqIzCaMtVoNewsNE2Xhzjv1y1jg/d9zjHY9aCHC+OxW4PW+zd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\nLNOz4tC4AAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x10d7b9210>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "simple_colocalisation(images[999])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{('Gene Symbol', 'CDC14'): [('Phenotype Term Accession', 'CMPO_0000427'),\n",
       "  ('Phenotype Term Accession', 'CMPO_0000397'),\n",
       "  ('Phenotype', 'altered kinetochore foci'),\n",
       "  ('Phenotype Term Name', 'protein localized in nucleolus phenotype'),\n",
       "  ('Phenotype Term Name', 'kinetochore phenotype'),\n",
       "  ('Phenotype Term Accession URL', 'http://www.ebi.ac.uk/cmpo/CMPO_0000397'),\n",
       "  ('Phenotype', 'GFP localization: nucleolus'),\n",
       "  ('Phenotype Term Accession URL', 'http://www.ebi.ac.uk/cmpo/CMPO_0000427')],\n",
       " ('Gene Symbol', 'cdc14'): [('Phenotype Term Accession', 'CMPO_0000416'),\n",
       "  ('Phenotype Term Accession URL', 'http://www.ebi.ac.uk/cmpo/CMPO_0000416'),\n",
       "  ('Phenotype', 'defective cell-cell aggregation'),\n",
       "  ('Phenotype Term Name', 'fewer aggregated cells in population phenotype')]}"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "args = {\n",
    "    \"name\": \"Gene Symbol\",\n",
    "    \"value\": \"cdc14\",\n",
    "    \"ns\": \"openmicroscopy.org/mapr/gene\",\n",
    "    \"ns2\": \"openmicroscopy.org/mapr/phenotype\",\n",
    "    # \"name2\": \"Phenotype Term Accession\", # optional\n",
    "}\n",
    "attributes_by_attributes(conn, **args)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Close the connection to IDR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "conn.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### License\n",
    "Copyright (C) 2016-2019 University of Dundee. All Rights Reserved.\n",
    "This program is free software; you can redistribute it and/or modify it\n",
    "under the terms of the GNU General Public License as published by the\n",
    "Free Software Foundation; either version 2 of the License, or\n",
    "(at your option) any later version.\n",
    "This program is distributed in the hope that it will be useful, but\n",
    "WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY\n",
    "or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for\n",
    "more details. You should have received a copy of the GNU General\n",
    "Public License along with this program; if not, write to the\n",
    "Free Software Foundation,\n",
    "Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA."
   ]
  }
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