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Update notebooks with the upcoming changes in v0.3
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@gtca
gtca committed Jul 3, 2024
1 parent cdbba38 commit eb8dd9d
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34 changes: 16 additions & 18 deletions docs/source/notebooks/annotations_management.ipynb
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{
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"<pre>MuData object with n_obs × n_vars = 60 × 100\n",
"<pre>MuData object with n_obs × n_vars = 60 × 100 (shared var) \n",
" 3 modalities\n",
" mod1:\t10 x 100\n",
" obs:\t&#x27;dataset&#x27;\n",
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" obs:\t&#x27;dataset&#x27;, &#x27;species&#x27;, &#x27;reference&#x27;</pre>"
],
"text/plain": [
"MuData object with n_obs × n_vars = 60 × 100\n",
"MuData object with n_obs × n_vars = 60 × 100 (shared var) \n",
" 3 modalities\n",
" mod1:\t10 x 100\n",
" obs:\t'dataset'\n",
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{
"data": {
"text/html": [
"<pre>MuData object with n_obs × n_vars = 10 × 100\n",
"<pre>MuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t10 x 100\n",
" obs:\t&#x27;status&#x27;\n",
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" var:\t&#x27;filtered&#x27;</pre>"
],
"text/plain": [
"MuData object with n_obs × n_vars = 10 × 100\n",
"MuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t10 x 100\n",
" obs:\t'status'\n",
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{
"data": {
"text/html": [
"<pre>MuData object with n_obs × n_vars = 10 × 300\n",
"<pre>MuData object with n_obs × n_vars = 10 × 300 (shared obs and var) \n",
" obs:\t&#x27;dataset&#x27;\n",
" 2 modalities\n",
" mod1:\tMuData object with n_obs × n_vars = 10 × 300\n",
" mod1:\tMuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t10 x 100\n",
" obs:\t&#x27;status&#x27;\n",
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" mod2:\t10 x 200</pre>"
],
"text/plain": [
"MuData object with n_obs × n_vars = 10 × 300\n",
"MuData object with n_obs × n_vars = 10 × 300 (shared obs and var) \n",
" obs:\t'dataset'\n",
" 2 modalities\n",
" mod1:\tMuData object with n_obs × n_vars = 10 × 300\n",
" mod1:\tMuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t10 x 100\n",
" obs:\t'status'\n",
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"name": "stdout",
"output_type": "stream",
"text": [
"{'mod1': MuData object with n_obs × n_vars = 10 × 100\n",
" 2 modalities\n",
" raw:\t10 x 100\n",
" obs:\t'status'\n",
" qced:\t8 x 50\n",
" obs:\t'status', 'filtered'\n",
" var:\t'filtered', 'mod2': AnnData object with n_obs × n_vars = 10 × 200}\n"
"MuData\n",
"├─ mod1 MuData [shared obs and var] (10 × 100)\n",
"│ ├─ raw AnnData (10 x 100)\n",
"│ └─ qced AnnData (8 x 50)\n",
"└─ mod2 AnnData (10 x 200)\n"
]
}
],
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],
"metadata": {
"kernelspec": {
"display_name": "ad0.9 (issue126)",
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"language": "python",
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"name": "main"
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"codemirror_mode": {
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.0"
"version": "3.12.3"
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"nbformat": 4,
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16 changes: 8 additions & 8 deletions docs/source/notebooks/axes.ipynb
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"metadata": {},
"outputs": [],
"source": [
"! pip install mudata"
"%pip install mudata"
]
},
{
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"name": "stderr",
"output_type": "stream",
"text": [
"/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/_core/mudata.py:445: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
"/usr/local/opt/[email protected]/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",
" warnings.warn(\n"
]
},
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{
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"<pre>MuData object with n_obs × n_vars = 600 × 1000\n",
"<pre>MuData object with n_obs × n_vars = 600 × 1000 (shared var) \n",
" 2 modalities\n",
" dat1:\t100 x 1000\n",
" dat2:\t500 x 1000</pre>"
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"MuData object with n_obs × n_vars = 600 × 1000\n",
"MuData object with n_obs × n_vars = 600 × 1000 (shared var) \n",
" 2 modalities\n",
" dat1:\t100 x 1000\n",
" dat2:\t500 x 1000"
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{
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"<pre>MuData object with n_obs × n_vars = 100 × 900\n",
"<pre>MuData object with n_obs × n_vars = 100 × 900 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t100 x 900\n",
" preproc:\t100 x 300</pre>"
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"MuData object with n_obs × n_vars = 100 × 900\n",
"MuData object with n_obs × n_vars = 100 × 900 (shared obs and var) \n",
" 2 modalities\n",
" raw:\t100 x 900\n",
" preproc:\t100 x 300"
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],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
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"toc": {
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