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W_SpreadsheetDataReader
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@yasinthanvickneswaran
yasinthanvickneswaran committed Feb 8, 2024
1 parent fa254e7 commit 8c85aef
Showing 1 changed file with 35 additions and 6 deletions.
41 changes: 35 additions & 6 deletions examples/test/Comparison.ipynb
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"cells": [
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 1,
"id": "481d3c70-313a-4979-8475-d4a0089a8a0b",
"metadata": {
"tags": []
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"text": [
"\n",
"****** Importing dataset SpreadsheetData using c302.SpreadsheetDataReader ******\n",
"c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"\n",
"****** Importing dataset UpdSpreadsheetData using c302.UpdatedSpreadsheetDataReader ******\n",
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"c302 >>> Total connections found 926 \n",
"\n",
"****** Importing dataset WormNeuroAtlas using c302.WormNeuroAtlasReader ******\n",
"*This version of the NeuroAtlas does not include the CAN neurons. This will be fixed soon.\n",
"*In loading the anatomical connectome, the following conventions are used to allow for its comparison with the other datasets: AWCL->AWCOFF and AWCR->AWCON\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\wormneuroatlas\\WormBase.py:52: UserWarning: Wormbase.org updated its database to a new version (WS291). The version of Worm Neuro Atlas that you are using has been built for the wormbase database version WS287. To ensure reproducible results, upgrade Worm Neuro Atlas with `python -m pip install --upgrade wormneuroatlas` If this warning persists after upgrading, let the developers know by opening an issue here: https://github.com/francescorandi/wormneuroatlas/issues. NOTE: You can still use Worm Neuro Atlas in the meantime. The metadata accessible via wormneuroatlas.WormBase.get_metadata() and wormneuroatlas.NeuroAtlas.get_metadata() contain the version of wormbase that you are currently using, so make sure you save the metadata alongside your results. \n",
" warnings.warn(w)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"c302 >>> Initialising WormNeuroAtlasReader\n",
"\n",
"****** Importing dataset Varshney using c302.VarshneyDataReader ******\n",
"c302 >>> Opened the Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n"
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"\n",
"****** Importing dataset Witvliet using c302.W_SpreadsheetDataReader ******\n",
"c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8_adult.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8_adult.xlsx\n"
]
}
],
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" \"UpdSpreadsheetData2\": \"c302.UpdatedSpreadsheetDataReader2\",\n",
" \"OpenWorm\": \"c302.OpenWormReader\",\n",
" \"WormNeuroAtlas\": \"c302.WormNeuroAtlasReader\",\n",
" \"Varshney\": \"c302.VarshneyDataReader\"}\n",
" \"Varshney\": \"c302.VarshneyDataReader\",\n",
" \"Witvliet\": \"c302.W_SpreadsheetDataReader\"}\n",
"\n",
"for name, reader in readers.items():\n",
"\n",
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},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 2,
"id": "2308051a-0a24-44db-a481-fc0d0f2af4fb",
"metadata": {
"tags": []
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" <th>OpenWorm</th>\n",
" <th>WormNeuroAtlas</th>\n",
" <th>Varshney</th>\n",
" <th>Witvliet</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
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" <td>302</td>\n",
" <td>300</td>\n",
" <td>281</td>\n",
" <td>222</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num Muscles</td>\n",
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" <td>95</td>\n",
" <td>0</td>\n",
" <td>97</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N->N conns</td>\n",
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" <td>5805</td>\n",
" <td>1650</td>\n",
" <td>6417</td>\n",
" <td>2496</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N with ->M</td>\n",
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" <td>159</td>\n",
" <td>0</td>\n",
" <td>127</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N->M conns</td>\n",
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" <td>926</td>\n",
" <td>0</td>\n",
" <td>564</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <td>N neurotransmitters</td>\n",
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" <td>Acetylcholine (2008)<br/>Acetylcholine_GJ (222)<br/>Acetylcholine_Tyramine (29)<br/>Acetylcholine_Tyramine_GJ (13)<br/>Dopamine (98)<br/>Dopamine_GJ (13)<br/>FMRFamide (170)<br/>FMRFamide_GJ (90)<br/>FRMFemide (45)<br/>FRMFemide_GJ (33)<br/>GABA (182)<br/>GABA_GJ (76)<br/>Generic_GJ (1356)<br/>Glutamate (824)<br/>Glutamate_GJ (324)<br/>Octapamine (19)<br/>Octapamine_GJ (4)<br/>Serotonin (163)<br/>Serotonin_Acetylcholine (91)<br/>Serotonin_Acetylcholine_GJ (13)<br/>Serotonin_GJ (20)<br/>Serotonin_Glutamate (11)<br/>Serotonin_Glutamate_GJ (1)<br/></td>\n",
" <td>Generic_GJ (1650)<br/></td>\n",
" <td>Chemical_Synapse (5386)<br/>Generic_GJ (1031)<br/></td>\n",
" <td>Chemical_Synapse (2186)<br/>Generic_GJ (310)<br/></td>\n",
" </tr>\n",
" <tr>\n",
" <td>M neurotransmitters</td>\n",
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" <td>Acetylcholine (924)<br/>Generic_GJ (2)<br/></td>\n",
" <td></td>\n",
" <td>**MISSING** (2)<br/>Acetylcholine (377)<br/>Acetylcholineplus_Tyramine (6)<br/>Dopamine (1)<br/>FMRFamide (3)<br/>FRMFemide (5)<br/>GABA (126)<br/>Glutamate (35)<br/>Serotonin (1)<br/>Serotoninplus_Acetylcholine (8)<br/></td>\n",
" <td>Chemical_Synapse (1)<br/></td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
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"<IPython.core.display.HTML object>"
]
},
"execution_count": 7,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
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