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@doc_params(scatter=doc_scatter)
def paga(
adata,
basis=None,
vkey="velocity",
color=None,
layer=None,
title=None,
threshold=None,
layout=None,
layout_kwds=None,
init_pos=None,
root=0,
labels=None,
single_component=False,
dashed_edges="connectivities",
solid_edges="transitions_confidence",
@doc_params(scatter=doc_scatter)
def tsne(adata, **kwargs):
"""\
Scatter plot in tsne basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
return scatter(adata, basis="tsne", **kwargs)
@doc_params(scatter=doc_scatter)
def pca(adata, **kwargs):
"""\
Scatter plot in pca basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
return scatter(adata, basis="pca", **kwargs)
@doc_params(scatter=doc_scatter)
def phate(adata, **kwargs):
"""\
Scatter plot in phate basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
return scatter(adata, basis="phate", **kwargs)
@doc_params(scatter=doc_scatter)
def velocity_embedding(
adata,
basis=None,
vkey="velocity",
density=None,
arrow_size=None,
arrow_length=None,
scale=None,
X=None,
V=None,
recompute=None,
color=None,
use_raw=None,
layer=None,
color_map=None,
colorbar=True,
@doc_params(scatter=doc_scatter)
def velocity_embedding_grid(
adata,
basis=None,
vkey="velocity",
density=None,
smooth=None,
min_mass=None,
arrow_size=None,
arrow_length=None,
arrow_color=None,
scale=None,
autoscale=True,
n_neighbors=None,
recompute=None,
X=None,
V=None,
@doc_params(scatter=doc_scatter)
def umap(adata, **kwargs):
"""\
Scatter plot in UMAP basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
return scatter(adata, basis="umap", **kwargs)
@doc_params(scatter=doc_scatter)
def draw_graph(adata, layout=None, **kwargs):
"""\
Scatter plot in draw_graph basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
if layout is None:
layout = f"{adata.uns['draw_graph']['params']['layout']}"
basis = f"draw_graph_{layout}"
if f"X_{basis}" not in adata.obsm_keys():
raise ValueError(f"Could not find draw_graph_{layout} in adata.obs.")
@doc_params(scatter=doc_scatter)
def trimap(adata, **kwargs):
"""\
Scatter plot in trimap basis.
Parameters
----------
{scatter}
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
"""
return scatter(adata, basis="trimap", **kwargs)
@doc_params(scatter=doc_scatter)
def velocity_embedding_stream(
adata,
basis=None,
vkey="velocity",
density=None,
smooth=None,
min_mass=None,
cutoff_perc=None,
arrow_color=None,
linewidth=None,
n_neighbors=None,
recompute=None,
color=None,
use_raw=None,
layer=None,
color_map=None,