"""plotting utilities that are built based on scSLAM-seq paper"""
from .scatters import scatters
from .scatters import docstrings
docstrings.delete_params("scatters.parameters", "adata", "basis")
[docs]@docstrings.with_indent(4)
def pca(adata, *args, **kwargs):
"""\
Scatter plot with pca basis.
Parameters
----------
adata: :class:`~anndata.AnnData`
an Annodata object.
%(scatters.parameters.no_adata|basis)s
Returns
-------
Nothing but plots the pca embedding of the adata object.
Examples
--------
>>> import dynamo as dyn
>>> adata = dyn.sample_data.hgForebrainGlutamatergic()
>>> adata = dyn.pp.recipe_monocle(adata)
>>> dyn.tl.dynamics(adata)
>>> dyn.pl.pca(
... adata,
... color='ntr'
... )
"""
scatters(adata, "pca", *args, **kwargs)
[docs]@docstrings.with_indent(4)
def umap(adata, *args, **kwargs):
"""\
Scatter plot with umap basis.
Parameters
----------
adata: :class:`~anndata.AnnData`
an Annodata object.
%(scatters.parameters.no_adata|basis)s
Returns
-------
Nothing but plots the umap embedding of the adata object.
Examples
--------
>>> import dynamo as dyn
>>> adata = dyn.sample_data.hgForebrainGlutamatergic()
>>> adata = dyn.pp.recipe_monocle(adata)
>>> dyn.tl.dynamics(adata)
>>> dyn.pl.umap(
... adata,
... color='ntr'
... )
"""
return scatters(adata, "umap", *args, **kwargs)
[docs]@docstrings.with_indent(4)
def trimap(adata, *args, **kwargs):
"""\
Scatter plot with trimap basis.
Parameters
----------
adata: :class:`~anndata.AnnData`
an Annodata object.
%(scatters.parameters.no_adata|basis)s
Returns
-------
Nothing but plots the pca embedding of the adata object.
Examples
--------
>>> import dynamo as dyn
>>> adata = dyn.sample_data.hgForebrainGlutamatergic()
>>> adata = dyn.pp.recipe_monocle(adata)
>>> dyn.tl.dynamics(adata)
>>> dyn.pl.trimap(
... adata,
... color='ntr'
... )
"""
return scatters(adata, "trimap", *args, **kwargs)
[docs]@docstrings.with_indent(4)
def tsne(adata, *args, **kwargs):
"""\
Scatter plot with tsne basis.
Parameters
----------
adata: :class:`~anndata.AnnData`
an Annodata object.
%(scatters.parameters.no_adata|basis)s
Returns
-------
Nothing but plots the tsne embedding of the adata object.
Examples
--------
>>> import dynamo as dyn
>>> adata = dyn.sample_data.hgForebrainGlutamatergic()
>>> adata = dyn.pp.recipe_monocle(adata)
>>> dyn.tl.dynamics(adata)
>>> dyn.pl.tsne(
... adata,
... color='ntr'
... )
"""
return scatters(adata, "tsne", *args, **kwargs)
# add leidan, louvain, etc.