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static plotting for spatial data #437
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@@ -51,42 +51,42 @@ | |
from squidpy._constants._pkg_constants import Key | ||
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. what's a good way to only make certain params appearing in docs? scanpy uses this: what do you think? if agree can implement logic but also open to suggestions There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Docrep has something like: https://docrep.readthedocs.io/en/latest/?badge=latest#docrep.DocstringProcessor.delete_params, though I've never used it, am open for suggestions. |
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def spatial( | ||
def _spatial_plot( | ||
adata: AnnData, | ||
spatial_key: str = Key.obsm.spatial, | ||
library_id: _SeqStr = None, | ||
library_key: str | None = None, | ||
library_first: bool = True, | ||
shape: _AvailShapes | None = ScatterShape.CIRCLE.s, # type: ignore[assignment] | ||
scale_factor: _SeqFloat = None, | ||
size: _SeqFloat = None, | ||
size_key: str = Key.uns.size_key, | ||
crop_coord: Sequence[_CoordTuple] | _CoordTuple | None = None, | ||
bw: bool = False, | ||
alpha: Optional[float] = None, | ||
color: Sequence[str | None] | str | None = None, | ||
groups: _SeqStr = None, | ||
use_raw: bool | None = None, | ||
layer: str | None = None, | ||
alt_var: str | None = None, | ||
edges: bool = False, | ||
edges_width: float = 0.1, | ||
edges_color: str | Sequence[float] | Sequence[str] = "grey", | ||
connectivity_key: str = Key.obsp.spatial_conn(), | ||
palette: Palette_t = None, | ||
library_id: _SeqStr = None, | ||
library_key: str | None = None, | ||
library_first: bool = True, | ||
cmap: Colormap | str | None = None, | ||
cmap_kwargs: Mapping[str, _VBound | _Normalize] | None = None, | ||
palette: Palette_t = None, | ||
alpha: Optional[float] = None, | ||
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scale_factor: _SeqFloat = None, | ||
size: _SeqFloat = None, | ||
size_key: str = Key.uns.size_key, | ||
crop_coord: Sequence[_CoordTuple] | _CoordTuple | None = None, | ||
img: NDArrayA | Sequence[NDArrayA] | None = None, | ||
img_key: str | None = None, | ||
img_alpha: Optional[float] = None, | ||
img_cmap: Colormap | str | None = None, | ||
img_channel: int | None = None, | ||
bw: bool = False, | ||
edges: bool = False, | ||
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edges_width: float = 0.1, | ||
edges_color: str | Sequence[float] | Sequence[str] = "grey", | ||
connectivity_key: str = Key.obsp.spatial_conn(), | ||
frameon: Optional[bool] = None, | ||
title: _SeqStr = None, | ||
axis_label: _SeqStr = None, | ||
wspace: float | None = None, | ||
hspace: float = 0.25, | ||
ncols: int = 4, | ||
cmap_kwargs: Mapping[str, _VBound | _Normalize] | None = None, | ||
add_outline: bool = False, | ||
outline_width: Tuple[float, float] = (0.3, 0.05), | ||
outline_color: Tuple[str, str] = ("black", "white"), | ||
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Please find a better name for this function
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_sort_haystack
?