monkeybread.plot.embedding_zoom

monkeybread.plot.embedding_zoom(adata, left_pct=None, top_pct=None, width_pct=None, height_pct=None, color=None, mask=None, basis='spatial', show=True, unzoom_s=None, zoom_s=None, axs=None, fig=None, **kwargs)

Shows embeddings of cells neighboring other cells with zoomed focus.

Plots the results of monkeybread.calc.cell_neighbors(), highlighting the cell neighbors. Zooms in on a specific rectangle in the plot, based on fractional coordinate space, for higher-resolution viewing.

Parameters:

• adata (AnnData) – Annotated data matrix.

• left_pct (Optional[float] (default: None)) – The fraction of the plot width to use as the left bound of the zoomed-in rectangle, e.g. 0.1 represents 10% from the left of the plot.

• top_pct (Optional[float] (default: None)) – The fraction of the plot height to use as the upper bound of the zoomed-in rectangle, e.g. 0.3 represents 30% from the top of the plot.

• width_pct (Optional[float] (default: None)) – The fraction of the plot width to use for the zoomed-in rectangle, e.g. 0.5 represents a width half of the original plot.

• height_pct (Optional[float] (default: None)) – The fraction of the plot height to use for the zoomed-in rectangle, e.g. 0.25 represents a height 25% of the original plot.

• color (Optional[str] (default: None)) – Column in adata.obs used to color cells.

• mask (Union[List[bool], List[str], None] (default: None)) – A mask to apply to adata.obs.index. Can be a list of cell indices or a boolean mask with the same length as the index, as described in monkeybread.plot.embedding_filter().

• basis (Optional[str] (default: 'spatial')) – Coordinates in adata.obsm[X_{basis}] to use. Defaults to spatial.

• show (Optional[bool] (default: True)) – Whether to show the plot or return the Axes object.

• unzoom_s (Optional[float] (default: None)) – Dot-size in the zoomed-out figure passed to scanpy.pl.embedding().

• zoom_s (Optional[float] (default: None)) – Dot-size in the zoomed-in figure passed to scanpy.pl.embedding().

• kwargs – Keyword arguments that will be passed to scanpy.pl.embedding().

Return type:

Optional[Figure]

Returns:

: If show = True, returns nothing. Otherwise, returns the Figure object the plots are contained within.

Example