grassp.pl.aligned_umap

aligned_umap(data, data2, highlight_hits=None, highlight_annotation_col=None, aligned_umap_key='X_aligned_umap', data1_label='data1', data2_label='data2', color_by='perturbation', data1_color='#C7E8F9', data2_color='#FFCCC2', figsize=(8.25, 6), size=80, alpha=0.4, ax=None, show=None, save=None)

Plot aligned UMAP embeddings for two datasets.

Parameters:

data AnnData

First annotated data matrix

data2 AnnData

Second annotated data matrix

highlight_hits Union[List[str], ndarray[bool, Any], None] (default: None)

List of protein names or boolean mask to highlight trajectories between datasets

highlight_annotation_col Optional[str] (default: None)

Column in data.obs to use for highlighting specific proteins

aligned_umap_key str (default: 'X_aligned_umap')

Key in data.obsm containing aligned UMAP coordinates

data1_label str (default: 'data1')

Label for first dataset in legend

data2_label str (default: 'data2')

Label for second dataset in legend

color_by Literal['perturbation', 'cluster'] (default: 'perturbation')

Whether to color by ‘perturbation’ or ‘cluster’

data1_color str (default: '#C7E8F9')

Color for first dataset points if coloring by perturbation

data2_color str (default: '#FFCCC2')

Color for second dataset points if coloring by perturbation

figsize tuple[float, float] (default: (8.25, 6))

Size of the figure in inches

size int (default: 80)

Size of scatter points

alpha float (default: 0.4)

Transparency of scatter points

ax Optional[Axes] (default: None)

Matplotlib axes to plot on

show Optional[bool] (default: None)

Whether to display the plot

save Union[bool, str, None] (default: None)

Whether to save the plot and optional filename

Return type:

Axes | None

Returns:

matplotlib.pyplot.Axes or None If show=False returns the axes object, otherwise returns None