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@michaelkyu
michaelkyu committed Dec 12, 2018
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46 changes: 24 additions & 22 deletions examples/Load_example_datasets.ipynb
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"text": [
"NDEx download time (sec): 241.07130336761475\n",
"Read HTTP response as JSON simplejson time (sec): 357.84295129776\n",
"loop time (sec): 38.50523900985718\n"
"NDEx download and CX parse time (sec): 356.6890811920166\n",
"Dim: (19009, 19009)\n",
"Bytes: 2890736648\n",
"Iterate through CX and construct array time (sec): 14.676801204681396\n"
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"[5 rows x 19009 columns]"
]
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"## Download human gene-gene similarity network from NDEx\n",
"## -- WARNING: This network is very large (19,009-by-19,009 matrix).\n",
"## -- Downloading will take ~10 min for a fast internet connection.\n",
"## -- *** Requires about 7 Gb to download and process **\n",
"## -- *** Requires ~6 GB of RAM to download and process ***\n",
"## -- *** ~4 GB of data is downloaded from NDEx, which takes ~10 min for a fast internet connection ***\n",
"## -- This requires the simplejson package (see previous cell)\n",
"sim, sim_names = ddot.ndex_to_sim_matrix(\n",
" ndex_url=ddot.HUMAN_GENE_SIMILARITIES_URL,\n",
" input_fmt='cx_matrix',\n",
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"hydronephrosis http://hiview.ucsd.edu/1b21bc44-f775-11e8-aaa6... "
]
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39 changes: 21 additions & 18 deletions examples/Make_disease_gene_ontologies.ipynb
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"text": [
"NDEx download time (sec): 457.28141617774963\n",
"Read HTTP response as JSON simplejson time (sec): 563.9876594543457\n",
"loop time (sec): 27.282840967178345\n"
"NDEx download and CX parse time (sec): 356.2376916408539\n",
"Dim: (19009, 19009)\n",
"Bytes: 2890736648\n",
"Iterate through CX and construct array time (sec): 14.60573434829712\n"
]
},
{
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}
],
"source": [
"## Read gene similarity network\n",
"## Download human gene-gene similarity network from NDEx\n",
"## -- WARNING: This network is very large (19,009-by-19,009 matrix).\n",
"## -- *** Requires ~6 GB of RAM to download and process ***\n",
"## -- *** ~4 GB of data is downloaded from NDEx, which takes ~10 min for a fast internet connection ***\n",
"## -- This requires the simplejson package (see previous cell)\n",
"sim, sim_names = ddot.ndex_to_sim_matrix(\n",
" ndex_url=ddot.HUMAN_GENE_SIMILARITIES_URL,\n",
" input_fmt='cx_matrix',\n",
" output_fmt='matrix',\n",
" subset=None)\n",
" output_fmt='matrix')\n",
"sim = pd.DataFrame(sim, columns=sim_names, index=sim_names)\n",
"\n",
"## Rank transform the similarities\n",
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"# # Retrieve a table of gene-disease associations from the Monarch Initiative (reformatted and stored on NDEx)\n",
"# monarch, _ = ddot.ndex_to_sim_matrix(\n",
"# ddot.config.MONARCH_DISEASE_GENE_SLIM_URL,\n",
"# similarity=None,\n",
"# input_fmt='cx',\n",
"# output_fmt='sparse')\n",
"# print(monarch.head())\n",
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