gedi2py.plotting.features

gedi2py.plotting.features(adata, features, *, basis='X_gedi_umap', layer=None, cmap='viridis', vmin=None, vmax=None, size=None, alpha=1.0, ncols=4, figsize=None, show=None, save=None, return_fig=False)[source]

Plot gene expression on GEDI embedding.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • features (Union[str, Sequence[str]]) – Gene name(s) to plot.

  • basis (str, default: 'X_gedi_umap') – Key in adata.obsm for embedding coordinates.

  • layer (str | None, default: None) – Layer to use for expression values. If None, uses adata.X.

  • cmap (str, default: 'viridis') – Colormap for expression values.

  • vmin (float | None, default: None) – Minimum value for color scale.

  • vmax (float | None, default: None) – Maximum value for color scale.

  • size (float | None, default: None) – Point size. If None, automatically determined.

  • alpha (float, default: 1.0) – Point transparency.

  • ncols (int, default: 4) – Number of columns for multi-panel plots.

  • figsize (tuple[float, float] | None, default: None) – Figure size.

  • show (bool | None, default: None) – If True, show the figure.

  • save (str | None, default: None) – Path to save the figure.

  • return_fig (bool, default: False) – If True, return the figure.

Return type:

Figure if ``return_fig=True``, else ``None`.`

Examples

>>> import gedi2py as gd
>>> gd.pl.features(adata, ["CD4", "CD8A", "FOXP3"])