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Merged
Zethson merged 6 commits into from
May 22, 2024
Merged

⬆️ add pandas 2 support #72

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835c036
:arrow_up: add pandas 2 support
May 20, 2024
016ce1c
:bento: run notebooks
May 20, 2024
367aa50
:lipstick: reformat with precommit
May 20, 2024
577fd37
:wrench: Move pandas down in deps
May 20, 2024
bee7ca8
:wrench: remove version req from pandas
May 20, 2024
b2851cf
:lipstick: precommit run
May 20, 2024
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14 changes: 12 additions & 2 deletions docs/tutorials/preprocessing.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,8 @@
"In the next step, we normalize the data. By default, normalization is an inplace operation, i.e. we only create a new anndata object, if we set the argument `inplace=False`. We demonstrate three different normalization methods that are build in `pytometry`:\n",
"* arcsinh \n",
"* logicle \n",
"* bi-exponential"
"* bi-exponential\n",
"* auto-logicle"
]
},
{
Expand Down Expand Up @@ -216,6 +217,15 @@
"source": [
"adata_biex = pm.tl.normalize_biExp(adata, inplace=False)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"adata_autologicle = pm.tl.normalize_autologicle(adata, inplace=False)"
]
}
],
"metadata": {
Expand All @@ -234,7 +244,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"version": "3.9.19"
},
"vscode": {
"interpreter": {
Expand Down
22 changes: 20 additions & 2 deletions docs/tutorials/quickstart.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,8 @@
"source": [
"import pytometry as pm\n",
"import readfcs\n",
"import anndata"
"import anndata\n",
"from matplotlib import rcParams"
]
},
{
Expand Down Expand Up @@ -114,7 +115,16 @@
"metadata": {},
"outputs": [],
"source": [
"pm.pl.scatter_density(adata, x_lim=[-1, 2.7e5])"
"rcParams[\"figure.figsize\"] = (6, 5)\n",
"pm.pl.scatter_density(adata, x_lim=[-5e3, 2e5], y_lim=[-5e3, 2e5])"
]
},
{
"cell_type": "markdown",
"id": "29e11870",
"metadata": {},
"source": [
"Compensate with the compensation matrix that is deposited in the FCS file. The `compensate` function also accepts a custom compensation matrix. "
]
},
{
Expand All @@ -127,6 +137,14 @@
"pm.pp.compensate(adata)"
]
},
{
"cell_type": "markdown",
"id": "2200fd8d",
"metadata": {},
"source": [
"For normalization, `pytometry` provides several different approaches:"
]
},
{
"cell_type": "code",
"execution_count": null,
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3 changes: 2 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ requires-python = '>= 3.9'
dependencies = [
"numpy>=1.20.0",
"numba>=0.57",
"pandas<2.0.0,>=1.5.3",
"pandas",
"anndata",
"scanpy",
"scipy",
Expand All @@ -25,6 +25,7 @@ dependencies = [
"flowutils",
"consensusclustering",
"minisom"

]

[project.urls]
Expand Down