Source code for dynamo.plot.dimension_reduction

"""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.