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Add more information on how to save plots #177

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9f425a0
Add how to save plots
Zethson Jun 6, 2025
5849f3e
Add how to save plots
Zethson Jun 6, 2025
8e00884
Add sphinx_design
Zethson Jun 7, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ _issues.ipynb
figures/*
data/*
write/*
plotting/CD79A.png

*.egg-info/
.pytest_cache/
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13 changes: 13 additions & 0 deletions basic-scrna-tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -639,6 +639,19 @@
"sc.pl.umap(adata, color=[\"leiden\"])"
]
},
{
"cell_type": "markdown",
"id": "90e510c8",
"metadata": {},
"source": [
"```{dropdown} How do I save a plot?\n",
"You can save a plot by directly accessing the returned Matplotlib figure:\n",
"````python\n",
"sc.pl.umap(adata, color=[\"leiden\"], show).figure.savefig(\"output_path.ext\")\n",
"````\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "7d7410a1-333a-4f21-b53e-91af768b07c7",
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5 changes: 1 addition & 4 deletions conf.py
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Expand Up @@ -23,10 +23,7 @@
copyright = f"{datetime.now():%Y}, {author}"
release = version = meta["Version"]

extensions = [
"myst_nb",
"sphinx.ext.intersphinx",
]
extensions = ["myst_nb", "sphinx.ext.intersphinx", "sphinx_design"]
myst_enable_extensions = [
"colon_fence",
]
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3 changes: 1 addition & 2 deletions paga-paul15.ipynb
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Expand Up @@ -864,7 +864,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -913,7 +913,6 @@
" fontsize=12,\n",
" frameon=False,\n",
" edges=True,\n",
" save=True,\n",
")"
]
},
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6 changes: 2 additions & 4 deletions pbmc3k.ipynb
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Expand Up @@ -1663,7 +1663,7 @@
},
{
"cell_type": "code",
"execution_count": 49,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -1690,9 +1690,7 @@
}
],
"source": [
"sc.pl.umap(\n",
" adata, color=\"leiden\", legend_loc=\"on data\", title=\"\", frameon=False, save=\".pdf\"\n",
")"
"sc.pl.umap(adata, color=\"leiden\", legend_loc=\"on data\", title=\"\", frameon=False)"
]
},
{
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643 changes: 523 additions & 120 deletions plotting/core.ipynb
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Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -11,6 +11,7 @@ dependencies = [
"sphinx",
"myst-nb",
"scanpydoc[theme]>=0.13.4",
"sphinx_design"
]

[tool.hatch.version]
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