grassp.pl.umap

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grassp.pl.umap#

umap(adata, highlight=None, annotate_by=None, highlight_edgecolor='black', highlight_linewidth=1.5, annotate_fontsize=8, annotate_color='black', annotate_offset=(5, 5), annotate_fontoutline=2, annotate_adjust=True, adjust_text_kwargs=None, ax=None, show=None, save=None, **kwargs)[source]#

Wrapper around sc.pl.umap that highlights specific observations with outlined markers.

This function creates a UMAP plot using scanpy’s plotting function and adds the ability to highlight specific observations (e.g., proteins) with a black outline and optionally annotate them with text labels from a specified column.

Parameters:
adata AnnData

Annotated data matrix with UMAP coordinates in .obsm[‘X_umap’].

highlight Optional[Sequence[str]] (default: None)

List of observation names (from adata.obs_names) to highlight with outlines. If None, no observations are highlighted.

annotate_by str | None (default: None)

Column name in adata.obs to use for annotating highlighted observations. If None, no annotations are added. Only highlighted observations are annotated.

highlight_edgecolor str (default: 'black')

Color of the outline around highlighted points.

highlight_linewidth float (default: 1.5)

Width of the outline around highlighted points.

annotate_fontsize float | int (default: 8)

Font size for annotation text.

annotate_color str (default: 'black')

Color of annotation text.

annotate_offset tuple[float, float] (default: (5, 5))

Tuple of (x, y) offset in points for annotation text positioning relative to the highlighted markers. Only used if annotate_adjust is False.

annotate_fontoutline int | None (default: 2)

Width of the white outline drawn around annotation text, or None for no outline.

annotate_adjust bool (default: True)

If True, uses the adjustText library to automatically adjust label positions to avoid overlaps. If False, uses fixed offset positioning.

adjust_text_kwargs dict | None (default: None)

Additional keyword arguments passed to adjust_text(). Defaults to grey connector arrows. min_arrow_len is derived from the axes width unless given explicitly.

ax Axes | None (default: None)

A matplotlib axes object. If None, uses current axes.

show bool | None (default: None)

Whether to show the figure. If None, uses scanpy settings.

save bool | str | None (default: None)

If True or a string, save the figure. A string is used as filename.

**kwargs

Additional keyword arguments passed to sc.pl.umap().

Return type:

Axes | None

Returns:

If show==False, returns matplotlib axes object. Otherwise returns None.

Examples

>>> import grassp as gr
>>> adata = gr.datasets.itzhak_2016()
>>> adata.obs.set_index("Lead ID", inplace=True)
>>> # Highlight specific proteins with annotation
>>> gr.pl.umap(
...    adata,
...    color="compartment",
...    highlight=["P00533", "P29353"],
...    annotate_by="Lead gene name")
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