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DOC: Update notebooks again re: doc text changes
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I think I was in the wrong Q2 environment for the last commit
for these notebooks, so the wrong --p-extreme-feature-count help
text was used. Should be good now.

Also, this updates these notebooks re: the doc text changes from
the prior commit.

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@fedarko
fedarko committed May 2, 2019
1 parent 45b3162 commit 01e531b
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25 changes: 17 additions & 8 deletions example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb
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Expand Up @@ -156,8 +156,9 @@
"text": [
"Usage: qiime rankratioviz unsupervised-rank-plot [OPTIONS]\r\n",
"\r\n",
" Generates an interactive visualization of DEICODE ranks in tandem with a\r\n",
" visualization of the log ratios of selected ranks' sample abundance.\r\n",
" Generates an interactive visualization of DEICODE feature rankings in\r\n",
" tandem with a visualization of the log ratios of selected features' sample\r\n",
" abundances.\r\n",
"\r\n",
"Options:\r\n",
" --i-ranks ARTIFACT PATH PCoAResults % Properties(['biplot'])\r\n",
Expand All @@ -180,11 +181,11 @@
" If specified, rankratioviz will only use\r\n",
" this many \"extreme\" features from either end\r\n",
" of all of the rankings. This is useful when\r\n",
" dealing with huge datasets (e.g. with over\r\n",
" 10,000 ranked features), for which running\r\n",
" rankratioviz normally might take a long\r\n",
" amount of time or crash due to memory\r\n",
" limits. [optional]\r\n",
" dealing with huge datasets (e.g. with BIOM\r\n",
" 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",
" --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",
Expand Down Expand Up @@ -279,7 +280,15 @@
"text": [
"Usage: rankratioviz [OPTIONS]\r\n",
"\r\n",
" Generates a plot of ranked taxa/metabolites and their abundances.\r\n",
" Generates a visualization of feature rankings and log ratios.\r\n",
"\r\n",
" The resulting visualization contains two plots. The first plot shows how\r\n",
" features are ranked, and the second plot shows the log ratio of \"selected\"\r\n",
" features' abundances within samples.\r\n",
"\r\n",
" The visualization is interactive, so which features are \"selected\" to\r\n",
" construct log ratios -- as well as various other properties of the\r\n",
" visualization -- can be changed by the user.\r\n",
"\r\n",
"Options:\r\n",
" -r, --ranks TEXT Differentials output from songbird or\r\n",
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31 changes: 20 additions & 11 deletions example_notebooks/songbird_red_sea/songbird_example.ipynb
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Expand Up @@ -124,8 +124,9 @@
"text": [
"Usage: qiime rankratioviz supervised-rank-plot [OPTIONS]\r\n",
"\r\n",
" Generates an interactive visualization of songbird ranks in tandem with a\r\n",
" visualization of the log ratios of selected ranks' sample abundance.\r\n",
" Generates an interactive visualization of songbird feature rankings in\r\n",
" tandem with a visualization of the log ratios of selected features' sample\r\n",
" abundances.\r\n",
"\r\n",
"Options:\r\n",
" --i-ranks ARTIFACT PATH FeatureData[Differential]\r\n",
Expand All @@ -148,11 +149,11 @@
" If specified, rankratioviz will only use\r\n",
" this many \"extreme\" features from either end\r\n",
" of all of the rankings. This is useful when\r\n",
" dealing with huge datasets (e.g. with over\r\n",
" 10,000 ranked features), for which running\r\n",
" rankratioviz normally might take a long\r\n",
" amount of time or crash due to memory\r\n",
" limits. [optional]\r\n",
" dealing with huge datasets (e.g. with BIOM\r\n",
" 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",
" --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",
Expand Down Expand Up @@ -221,8 +222,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"2019-05-02 16:06:44.378676: 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",
"2019-05-02 16:06:44.379041: 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",
"2019-05-02 16:36:02.984287: 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",
"2019-05-02 16:36:02.984675: 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",
Expand All @@ -241,7 +242,7 @@
"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 [00:15<00:00, 503.83it/s]\r\n"
"100%|██████████████████████████████████████| 8000/8000 [00:12<00:00, 631.31it/s]\r\n"
]
}
],
Expand Down Expand Up @@ -274,7 +275,15 @@
"text": [
"Usage: rankratioviz [OPTIONS]\r\n",
"\r\n",
" Generates a plot of ranked taxa/metabolites and their abundances.\r\n",
" Generates a visualization of feature rankings and log ratios.\r\n",
"\r\n",
" The resulting visualization contains two plots. The first plot shows how\r\n",
" features are ranked, and the second plot shows the log ratio of \"selected\"\r\n",
" features' abundances within samples.\r\n",
"\r\n",
" The visualization is interactive, so which features are \"selected\" to\r\n",
" construct log ratios -- as well as various other properties of the\r\n",
" visualization -- can be changed by the user.\r\n",
"\r\n",
"Options:\r\n",
" -r, --ranks TEXT Differentials output from songbird or\r\n",
Expand Down

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