"""plotting utilities that are built based on scSLAM-seq paper"""
from typing import Optional, Union
from anndata import AnnData
from matplotlib.axes import Axes
from .scatters import docstrings, scatters
docstrings.delete_params("scatters.parameters", "adata", "basis")
[docs]def pca(adata: AnnData, *args, **kwargs) -> Optional[Axes]:
"""Scatter plot with pca basis.
Args:
adata: an AnnData object.
*args: any other positional arguments passed to `dynamo.pl.scatters`.
**kwargs: any other keyword arguments passed to `dynamo.pl.scatters`.
Returns:
None would be returned in default and the plotted figure would be shown directly. If set
`save_show_or_return='return'` as a kwarg, the axes of the plot would be returned.
"""
return scatters(adata, "pca", *args, **kwargs)
[docs]def umap(adata: AnnData, *args, **kwargs) -> Optional[Axes]:
"""Scatter plot with umap basis.
Args:
adata: an AnnData object.
*args: any other positional arguments passed to `dynamo.pl.scatters`.
**kwargs: any other keyword arguments passed to `dynamo.pl.scatters`.
Returns:
None would be returned in default and the plotted figure would be shown directly. If set
`save_show_or_return='return'` as a kwarg, the axes of the plot would be returned.
"""
return scatters(adata, "umap", *args, **kwargs)
[docs]def trimap(adata: AnnData, *args, **kwargs):
"""Scatter plot with trimap basis.
Args:
adata: an AnnData object.
*args: any other positional arguments passed to `dynamo.pl.scatters`.
**kwargs: any other keyword arguments passed to `dynamo.pl.scatters`.
Returns:
None would be returned in default and the plotted figure would be shown directly. If set
`save_show_or_return='return'` as a kwarg, the axes of the plot would be returned.
"""
return scatters(adata, "trimap", *args, **kwargs)
[docs]def tsne(adata: AnnData, *args, **kwargs):
"""Scatter plot with tsne basis.
Args:
adata: an AnnData object.
*args: any other positional arguments passed to `dynamo.pl.scatters`.
**kwargs: any other keyword arguments passed to `dynamo.pl.scatters`.
Returns:
None would be returned in default and the plotted figure would be shown directly. If set
`save_show_or_return='return'` as a kwarg, the axes of the plot would be returned.
"""
return scatters(adata, "tsne", *args, **kwargs)
# add leidan, louvain, etc.