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DOC: Update example ipynbs re: recent API changes
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fedarko committed May 13, 2019
1 parent 9598ace commit d380931
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20 changes: 19 additions & 1 deletion example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb
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" tables exceeding 1 million entries), for\r\n",
" which running rankratioviz normally might\r\n",
" take a long amount of time or crash due to\r\n",
" memory limits. [optional]\r\n",
" memory limits. Additionally, following this\r\n",
" feature-filtering step, all \"empty\" samples\r\n",
" (i.e. those containing zeroes for every\r\n",
" remaining feature) will be removed from the\r\n",
" visualization. [optional]\r\n",
" --o-visualization VISUALIZATION PATH\r\n",
" [required if not passing --output-dir]\r\n",
" --output-dir DIRECTORY Output unspecified results to a directory\r\n",
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" (i.e. those containing zeroes for every\r\n",
" remaining feature) will be removed from the\r\n",
" visualization.\r\n",
" -gnps, --assume-gnps-feature-metadata\r\n",
" If specified, rankratioviz will assume that\r\n",
" the input feature metadata was obtained from\r\n",
" GNPS. This means that rankratioviz will read\r\n",
" each feature's ID as \"A;B\", where A is the\r\n",
" mass-to-charge ratio of the feature\r\n",
" (corresponding to the \"parent mass\" column\r\n",
" in the feature metadata) and B is the\r\n",
" discharge time of the feature (corresponding\r\n",
" to the \"RTConsensus\" column in the feature\r\n",
" metadata). rankratioviz will then only\r\n",
" annotate feature IDs with their\r\n",
" corresponding \"LibraryID\" column in the\r\n",
" feature metadata file.\r\n",
" -v, --verbose If passed, this will output debug messages.\r\n",
" --help Show this message and exit.\r\n"
]
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26 changes: 22 additions & 4 deletions example_notebooks/songbird_red_sea/songbird_example.ipynb
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Expand Up @@ -153,7 +153,11 @@
" tables exceeding 1 million entries), for\r\n",
" which running rankratioviz normally might\r\n",
" take a long amount of time or crash due to\r\n",
" memory limits. [optional]\r\n",
" memory limits. Additionally, following this\r\n",
" feature-filtering step, all \"empty\" samples\r\n",
" (i.e. those containing zeroes for every\r\n",
" remaining feature) will be removed from the\r\n",
" visualization. [optional]\r\n",
" --o-visualization VISUALIZATION PATH\r\n",
" [required if not passing --output-dir]\r\n",
" --output-dir DIRECTORY Output unspecified results to a directory\r\n",
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"name": "stdout",
"output_type": "stream",
"text": [
"2019-05-06 20:25:14.969262: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX\r\n",
"2019-05-06 20:25:14.969641: I tensorflow/core/common_runtime/process_util.cc:71] Creating new thread pool with default inter op setting: 8. Tune using inter_op_parallelism_threads for best performance.\r\n",
"2019-05-13 01:10:05.637409: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX\r\n",
"2019-05-13 01:10:05.637786: I tensorflow/core/common_runtime/process_util.cc:71] Creating new thread pool with default inter op setting: 8. Tune using inter_op_parallelism_threads for best performance.\r\n",
"WARNING:tensorflow:From /Users/mfedarko/Software/forks/songbird/songbird/multinomial.py:75: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version.\r\n",
"Instructions for updating:\r\n",
"Use tf.random.categorical instead.\r\n",
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"WARNING:tensorflow:From /anaconda3/envs/q2-2019.1/lib/python3.6/site-packages/tensorflow/python/ops/math_ops.py:3066: to_int32 (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version.\r\n",
"Instructions for updating:\r\n",
"Use tf.cast instead.\r\n",
"100%|██████████████████████████████████████| 8000/8000 [00:12<00:00, 616.12it/s]\r\n"
"100%|██████████████████████████████████████| 8000/8000 [00:13<00:00, 590.29it/s]\r\n"
]
}
],
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" (i.e. those containing zeroes for every\r\n",
" remaining feature) will be removed from the\r\n",
" visualization.\r\n",
" -gnps, --assume-gnps-feature-metadata\r\n",
" If specified, rankratioviz will assume that\r\n",
" the input feature metadata was obtained from\r\n",
" GNPS. This means that rankratioviz will read\r\n",
" each feature's ID as \"A;B\", where A is the\r\n",
" mass-to-charge ratio of the feature\r\n",
" (corresponding to the \"parent mass\" column\r\n",
" in the feature metadata) and B is the\r\n",
" discharge time of the feature (corresponding\r\n",
" to the \"RTConsensus\" column in the feature\r\n",
" metadata). rankratioviz will then only\r\n",
" annotate feature IDs with their\r\n",
" corresponding \"LibraryID\" column in the\r\n",
" feature metadata file.\r\n",
" -v, --verbose If passed, this will output debug messages.\r\n",
" --help Show this message and exit.\r\n"
]
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