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Zethsonflying-sheep
Zethson
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flying-sheep
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chore: deprecate save parameter of plots (#3675)
Co-authored-by: Phil Schaf <[email protected]>
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‎.gitignore‎

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# Scanpy outfiles
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/data/
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/write/
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/figures/
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# Docs
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/docs/_build/

‎docs/release-notes/3675.docs.md‎

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Update tutorial {doc}`/tutorials/experimental/dask` for {mod}`anndata` 0.12 (see {pr}`scverse/scanpy-tutorials#186`) {smaller}`I Gold`

‎docs/release-notes/3675.misc.md‎

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Deprecate `save` parameter of plotting functions. {smaller}`zethson`

‎notebooks‎

‎src/scanpy/_settings/__init__.py‎

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@@ -229,7 +229,7 @@ def datasetdir(cls, datasetdir: Path | str) -> None:
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@property
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def figdir(cls) -> Path:
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"""Directory for saving figures (default `'./figures/'`)."""
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r"""Directory for `autosave`\ ing figures (default `'./figures/'`)."""
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return cls._figdir
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@figdir.setter

‎src/scanpy/plotting/_anndata.py‎

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@@ -145,8 +145,9 @@ def scatter( # noqa: PLR0913
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marker: str | Sequence[str] = ".",
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title: str | Collection[str] | None = None,
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show: bool | None = None,
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save: str | bool | None = None,
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ax: Axes | None = None,
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# deprecated
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save: str | bool | None = None,
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) -> Axes | list[Axes] | None:
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"""Scatter plot along observations or variables axes.
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@@ -750,9 +751,9 @@ def violin( # noqa: PLR0912, PLR0913, PLR0915
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ylabel: str | Sequence[str] | None = None,
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rotation: float | None = None,
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show: bool | None = None,
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save: bool | str | None = None,
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ax: Axes | None = None,
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# deprecatd
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# deprecated
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save: bool | str | None = None,
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scale: DensityNorm | Empty = _empty,
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**kwds,
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) -> Axes | FacetGrid | None:
@@ -1007,7 +1008,7 @@ def clustermap(
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*,
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use_raw: bool | None = None,
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show: bool | None = None,
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save: bool | str | None = None,
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save: bool | str | None = None, # deprecated
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**kwds,
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) -> ClusterGrid | None:
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"""Hierarchically-clustered heatmap.

‎src/scanpy/plotting/_docs.py‎

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@@ -186,7 +186,8 @@
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save
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If `True` or a `str`, save the figure.
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A string is appended to the default filename.
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Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.\
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Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
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(deprecated in favour of `sc.pl.plot(show=False).figure.savefig()`).\
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"""
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doc_show_save_ax = f"""\

‎src/scanpy/plotting/_preprocessing.py‎

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@@ -21,8 +21,9 @@ def highly_variable_genes( # noqa: PLR0912
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*,
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log: bool = False,
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show: bool | None = None,
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save: bool | str | None = None,
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highly_variable_genes: bool = True,
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# deprecated
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save: bool | str | None = None,
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) -> None:
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"""Plot dispersions or normalized variance versus means for genes.
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@@ -111,6 +112,7 @@ def filter_genes_dispersion(
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*,
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log: bool = False,
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show: bool | None = None,
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# deprecated
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save: bool | str | None = None,
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) -> None:
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"""Plot dispersions versus means for genes.

‎src/scanpy/plotting/_stacked_violin.py‎

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@@ -682,7 +682,6 @@ def stacked_violin( # noqa: PLR0913
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categories_order: Sequence[str] | None = None,
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swap_axes: bool = False,
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show: bool | None = None,
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save: bool | str | None = None,
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return_fig: bool | None = False,
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ax: _AxesSubplot | None = None,
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vmin: float | None = None,
@@ -700,6 +699,7 @@ def stacked_violin( # noqa: PLR0913
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# deprecated
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order: Sequence[str] | None | Empty = _empty,
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scale: DensityNorm | Empty = _empty,
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save: bool | str | None = None,
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**kwds,
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) -> StackedViolin | dict | None:
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"""Stacked violin plots.

‎src/scanpy/plotting/_tools/__init__.py‎

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@@ -188,6 +188,7 @@ def pca_variance_ratio(
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*,
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log: bool = False,
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show: bool | None = None,
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# deprecated
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save: bool | str | None = None,
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):
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"""Plot the variance ratio.
@@ -230,9 +231,10 @@ def dpt_timeseries(
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*,
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color_map: str | Colormap | None = None,
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show: bool | None = None,
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save: bool | None = None,
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as_heatmap: bool = True,
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marker: str | Sequence[str] = ".",
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# deprecated
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save: bool | None = None,
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):
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"""Heatmap of pseudotime series.
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@@ -277,9 +279,10 @@ def dpt_groups_pseudotime(
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color_map: str | Colormap | None = None,
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palette: Sequence[str] | Cycler | None = None,
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show: bool | None = None,
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save: bool | str | None = None,
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marker: str | Sequence[str] = ".",
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return_fig: bool = False,
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# deprecated
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save: bool | str | None = None,
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) -> Figure | None:
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"""Plot groups and pseudotime.
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@@ -349,8 +352,8 @@ def rank_genes_groups( # noqa: PLR0912, PLR0913, PLR0915
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ncols: int = 4,
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sharey: bool = True,
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show: bool | None = None,
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save: bool | None = None,
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ax: Axes | None = None,
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save: bool | None = None, # deprecated
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**kwds,
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) -> list[Axes] | None:
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"""Plot ranking of genes.
@@ -503,7 +506,12 @@ def rank_genes_groups( # noqa: PLR0912, PLR0913, PLR0915
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def _fig_show_save_or_axes(
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plot_obj: BasePlot, *, return_fig: bool, show: bool | None, save: bool | None
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plot_obj: BasePlot,
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*,
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return_fig: bool,
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show: bool | None,
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# deprecated
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save: bool | None,
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):
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"""Decides what to return."""
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if return_fig:
@@ -528,9 +536,9 @@ def _rank_genes_groups_plot( # noqa: PLR0912, PLR0913, PLR0915
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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return_fig: bool = False,
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gene_symbols: str | None = None,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Call the different `rank_genes_groups_*` plots."""
@@ -703,7 +711,7 @@ def rank_genes_groups_heatmap(
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Plot ranking of genes using heatmap plot (see :func:`~scanpy.pl.heatmap`).
@@ -786,7 +794,7 @@ def rank_genes_groups_tracksplot(
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Plot ranking of genes using heatmap plot (see :func:`~scanpy.pl.heatmap`).
@@ -863,8 +871,8 @@ def rank_genes_groups_dotplot( # noqa: PLR0913
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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return_fig: bool = False,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Plot ranking of genes using dotplot plot (see :func:`~scanpy.pl.dotplot`).
@@ -1002,8 +1010,8 @@ def rank_genes_groups_stacked_violin( # noqa: PLR0913
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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return_fig: bool = False,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Plot ranking of genes using stacked_violin plot.
@@ -1090,8 +1098,8 @@ def rank_genes_groups_matrixplot( # noqa: PLR0913
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min_logfoldchange: float | None = None,
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key: str | None = None,
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show: bool | None = None,
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save: bool | None = None,
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return_fig: bool = False,
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save: bool | None = None, # deprecated
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**kwds,
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):
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"""Plot ranking of genes using matrixplot plot (see :func:`~scanpy.pl.matrixplot`).
@@ -1230,8 +1238,8 @@ def rank_genes_groups_violin( # noqa: PLR0913
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size: int = 1,
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ax: Axes | None = None,
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show: bool | None = None,
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save: bool | None = None,
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# deprecated
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save: bool | None = None,
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scale: DensityNorm | Empty = _empty,
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):
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"""Plot ranking of genes for all tested comparisons.
@@ -1348,8 +1356,9 @@ def sim(
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as_heatmap: bool = False,
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shuffle: bool = False,
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show: bool | None = None,
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save: bool | str | None = None,
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marker: str | Sequence[str] = ".",
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# deprecated
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save: bool | str | None = None,
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) -> None:
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"""Plot results of simulation.
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@@ -1456,9 +1465,9 @@ def embedding_density( # noqa: PLR0912, PLR0913, PLR0915
14561465
wspace: None = None,
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title: str | None = None,
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show: bool | None = None,
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save: bool | str | None = None,
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ax: Axes | None = None,
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return_fig: bool | None = None,
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save: bool | str | None = None, # deprecated
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**kwargs,
14631472
) -> Figure | Axes | None:
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"""Plot the density of cells in an embedding (per condition).

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