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Add matplotlib magic.
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Fix pathlib import.
Add changes to changelog.
morriscb committed Jul 11, 2024
1 parent b067b89 commit 205b71b
Showing 18 changed files with 1,679 additions and 957 deletions.
2 changes: 2 additions & 0 deletions intro.md
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@@ -59,6 +59,8 @@ Available notebooks:

## Release Notes
* **[abc_atlas_access (v0.1.2)]**
* Add matplotlib magic.
* Fixed bugs in pathlib import in notebooks
* Added script for selecting genes from expression matrices for use on
CodeOcean.
* **[abc_atlas_access (v0.1.1)]**
181 changes: 91 additions & 90 deletions notebooks/10x_snRNASeq_tutorial_part_1.ipynb

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57 changes: 36 additions & 21 deletions notebooks/10x_snRNASeq_tutorial_part_2a.ipynb
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@@ -1,5 +1,21 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"IPython magic command to render matplotlib plots."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%matplotlib inline"
]
},
{
"cell_type": "markdown",
"metadata": {},
@@ -15,11 +31,10 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"import pandas as pd\n",
"from pathlib import Path\n",
"import numpy as np\n",
@@ -42,7 +57,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"outputs": [
{
@@ -51,7 +66,7 @@
"'releases/20240330/manifest.json'"
]
},
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
@@ -68,7 +83,7 @@
},
{
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"metadata": {},
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"source": [
@@ -89,7 +104,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [
{
@@ -255,7 +270,7 @@
" WMB-10Xv3-TH 130454"
]
},
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
@@ -281,7 +296,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -290,7 +305,7 @@
"['WMB-10XMulti/log2', 'WMB-10XMulti/raw']"
]
},
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@@ -301,7 +316,7 @@
},
{
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"execution_count": 7,
"metadata": {},
"outputs": [
{
@@ -319,7 +334,7 @@
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{
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@@ -329,7 +344,7 @@
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"metadata": {},
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{
@@ -420,7 +435,7 @@
"ENSMUSG00000100241 Slc18a3"
]
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"execution_count": 9,
"metadata": {},
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}
@@ -436,46 +451,46 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"WMB-10XMulti\n",
" - time taken: 0.1000140000000016\n",
" - time taken: 0.1458529999999989\n",
"WMB-10Xv2-CTXsp\n"
]
},
{
"name": "stderr",
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"text": [
"WMB-10Xv2-CTXsp-log2.h5ad: 100%|██████████| 1.74G/1.74G [01:09<00:00, 24.9MMB/s] \n"
"WMB-10Xv2-CTXsp-log2.h5ad: 100%|███████████████████████████████████████████████████████████████████████████████████████| 1.74G/1.74G [01:08<00:00, 25.3MMB/s]\n"
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{
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"text": [
" - time taken: 2.0210620000000006\n",
" - time taken: 2.472235999999995\n",
"WMB-10Xv2-HPF\n"
]
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"text": [
"WMB-10Xv2-HPF-log2.h5ad: 100%|██████████| 6.10G/6.10G [04:48<00:00, 21.2MMB/s] \n"
"WMB-10Xv2-HPF-log2.h5ad: 100%|█████████████████████████████████████████████████████████████████████████████████████████| 6.10G/6.10G [04:05<00:00, 24.8MMB/s]\n"
]
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{
"name": "stdout",
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"text": [
" - time taken: 6.7627419999999745\n",
"total time taken: 140.118578\n"
" - time taken: 9.844729000000001\n",
"total time taken: 114.037751\n"
]
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],
@@ -517,7 +532,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 11,
"metadata": {},
"outputs": [
{
104 changes: 59 additions & 45 deletions notebooks/10x_snRNASeq_tutorial_part_2b.ipynb

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