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Add example for selecting a subset from a backed adata #117

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53 changes: 32 additions & 21 deletions docs/notebooks/demo_060121.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -68,15 +68,15 @@
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"processing: 100%|██████████| 1/1 [00:00<00:00, 1.14it/s]"
"processing: 100%|██████████| 1/1 [00:00<00:00, 1.10it/s]"
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Expand All @@ -130,7 +130,7 @@
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"outputs": [
Expand All @@ -139,8 +139,8 @@
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" total used free shared buff/cache available\r\n",
"Mem: 15Gi 9.0Gi 3.8Gi 880Mi 2.6Gi 5.1Gi\r\n",
"Swap: 2.0Gi 1.8Gi 250Mi\r\n"
"Mem: 15Gi 10Gi 504Mi 1.3Gi 4.7Gi 3.6Gi\r\n",
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Expand All @@ -150,17 +150,17 @@
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Expand All @@ -172,15 +172,15 @@
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"processing: 100%|██████████| 8/8 [00:01<00:00, 6.26it/s]"
"processing: 100%|██████████| 6/6 [00:01<00:00, 5.23it/s]"
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Expand All @@ -206,12 +206,24 @@
},
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"text": [
"AnnData object with n_obs × n_vars = 999 × 24057 backed at 'data/normalized_subset.h5ad'\n",
" var: 'highly_variable'\n",
" uns: 'hvg'\n"
]
}
],
"source": [
"my_normalized_adata = normalized_adata[1:1000,:]"
"# if wanting to work with a subset of data in backed mode (here choosing the first 1000 cells):\n",
"normalized_adata = normalized_adata[:1000,:].copy(filename='./data/normalized_subset.h5ad')\n",
"print(normalized_adata)"
]
},
{
Expand All @@ -227,15 +239,15 @@
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"text": [
"AnnData object with n_obs × n_vars = 1809 × 24057 backed at 'data/normalized16.h5ad'\n",
"AnnData object with n_obs × n_vars = 999 × 24057 backed at 'data/normalized_subset.h5ad'\n",
" var: 'highly_variable'\n",
" uns: 'hvg'\n"
]
Expand All @@ -259,15 +271,15 @@
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"text": [
"2021-07-14 23:09:48,849 root WARNING Ignoring svd_solver, using IncrementalPCA\n"
"2021-07-23 16:19:25,832 root WARNING Ignoring svd_solver, using IncrementalPCA\n"
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Expand Down Expand Up @@ -418,7 +430,6 @@
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