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Update slicing/updating example in the docs
Closes #80
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‎docs/source/notebooks/nuances.ipynb‎

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@@ -34,7 +34,15 @@
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n"
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]
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}
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],
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"source": [
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"%pip install mudata"
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]
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"<mudata._core.config.set_options at 0x148b0fa90>"
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]
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},
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"execution_count": 3,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"mudata.set_options(pull_on_update=False)"
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]
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},
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"cell_type": "code",
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"metadata": {},
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"source": [
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"import numpy as np\n",
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},
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{
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"name": "stderr",
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"text": [
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"/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/src/mudata/_core/mudata.py:869: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
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" warnings.warn(\n",
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"/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/src/mudata/_core/mudata.py:1478: UserWarning: Modality names will be prepended to var_names since there are identical var_names in different modalities.\n",
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"/usr/local/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/mudata/_core/mudata.py:1558: UserWarning: Modality names will be prepended to var_names since there are identical var_names in different modalities.\n",
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" warnings.warn(\n"
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]
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}
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},
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"execution_count": 7,
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{
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" dtype='object')"
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]
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"output_type": "execute_result"
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}
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"source": [
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"### Filtering data\n",
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"\n",
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"In rare cases some observations (or variables) can be dropped from all the contained modalities:"
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"In some cases some observations (or variables) can be dropped from all the contained modalities:"
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]
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"execution_count": 7,
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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"source": [
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"smaller_mdata = MuData({\n",
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" \"mod1\": mod1[:900].copy(),\n",
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" \"mod2\": mod2[:900].copy(),\n",
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"})"
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"mdata.obs[\"dummy_index\"] = range(len(mdata))\n",
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"\n",
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"smaller_mdata = mdata.copy()\n",
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"\n",
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"smaller_mdata.mod['mod1'] = mod1[:900]\n",
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"smaller_mdata.mod['mod2'] = mod2[:900]"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"While `smaller_mdata` includes `mod1` and `mod2` as its modalities, it currently does not know about this change:"
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"While `smaller_mdata` now includes modalities with fewer observations, it currently does not know about this change:"
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},
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{
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"cell_type": "code",
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{
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"data": {
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"text/html": [
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"<pre>MuData object with n_obs × n_vars = 900 × 300\n",
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"<pre>MuData object with n_obs × n_vars = 1000 × 300\n",
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" obs:\t&#x27;dummy_index&#x27;\n",
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" 2 modalities\n",
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" mod1:\t900 x 100\n",
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" mod2:\t900 x 200</pre>"
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"text/plain": [
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"MuData object with n_obs × n_vars = 900 × 300\n",
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"MuData object with n_obs × n_vars = 1000 × 300\n",
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" obs:\t'dummy_index'\n",
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" 2 modalities\n",
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" mod1:\t900 x 100\n",
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" mod2:\t900 x 200"
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"output_type": "execute_result"
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"smaller_mdata"
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]
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"999\n"
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]
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}
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],
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"source": [
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"print(max(smaller_mdata.obs['dummy_index']))"
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]
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},
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"<pre>MuData object with n_obs × n_vars = 900 × 300\n",
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" obs:\t&#x27;dummy_index&#x27;\n",
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" 2 modalities\n",
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" mod1:\t900 x 100\n",
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" mod2:\t900 x 200</pre>"
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"text/plain": [
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"MuData object with n_obs × n_vars = 900 × 300\n",
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" obs:\t'dummy_index'\n",
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" 2 modalities\n",
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" mod1:\t900 x 100\n",
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" mod2:\t900 x 200"
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"smaller_mdata"
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"execution_count": 12,
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"metadata": {},
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"output_type": "stream",
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"text": [
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"899\n"
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}
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],
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"source": [
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"print(max(smaller_mdata.obs['dummy_index']))"
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]
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"Index([], dtype='object')"
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"Index(['dummy_index'], dtype='object')"
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"<mudata._core.config.set_options at 0x3597fec00>"
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"<mudata._core.config.set_options at 0x1491e95d0>"
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"Index([], dtype='object')\n"
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"Index(['dummy_index'], dtype='object')\n"
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"Index(['mod1:mod1_profiled'], dtype='object')\n"
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"Index(['dummy_index', 'mod1:mod1_profiled'], dtype='object')\n"
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"Index(['mod1_profiled'], dtype='object')\n"
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"Index(['dummy_index', 'mod1_profiled'], dtype='object')\n"
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"name": "python",
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"version": "3.11.9"
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"toc": {
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