troutpy.pl.interactions_with_arrows

troutpy.pl.interactions_with_arrows#

troutpy.pl.interactions_with_arrows(sdata, layer='extracellular_transcripts_enriched', gene='Arc', gene_key='feature_name', cell_id_key='cell_id', color_target='blue', color_source='red', color_transcript='green', spatial_key='spatial', img=None, img_alpha=None, image_cmap=None, size=8, alpha=0.6, title=None, legend_loc='best', figsize=(10, 10), dpi=100, save=None, **kwargs)#

Plot arrows from source to target cells based on transcript proximity for a gene.

Source and target cells, and the transcript locations, are color-coded. An optional background image (e.g. a tissue section) can be overlaid behind the plot.

Parameters:

  • sdata (SpatialData) – Spatial data object containing the transcript and cell position data.

  • layer (str (default: 'extracellular_transcripts_enriched')) – The layer in sdata.points that contains the extracellular RNA transcript data, with closest_target_cell and closest_source_cell columns.

  • gene (str (default: 'Arc')) – The gene of interest.

  • gene_key (str (default: 'feature_name')) – The column name used to identify the gene in layer.

  • cell_id_key (str (default: 'cell_id')) – The column name in sdata["table"].obs used to identify individual cells.

  • color_target (str (default: 'blue')) – Color for the target cells.

  • color_source (str (default: 'red')) – Color for the source cells.

  • color_transcript (str (default: 'green')) – Color for the transcript locations.

  • spatial_key (str (default: 'spatial')) – The key in sdata["table"].obsm that stores the spatial coordinates of the cells.

  • img (Union[bool, Sequence, None] (default: None)) – Optional background image (e.g., tissue section) to display behind the plot.

  • img_alpha (Optional[float] (default: None)) – Transparency level for the background image. Ignored if img is None.

  • image_cmap (Optional[Colormap] (default: None)) – Colormap for the background image.

  • size (float | Sequence[float] | None (default: 8)) – Size of the plotted points (cells and transcripts).

  • alpha (float (default: 0.6)) – Transparency level for the plotted points.

  • title (Union[str, Sequence[str], None] (default: None)) – Title of the plot. If None, the gene name is used.

  • legend_loc (str | None (default: 'best')) – Location of the legend on the plot.

  • figsize (tuple[float, float] (default: (10, 10))) – Size of the plot.

  • dpi (int | None (default: 100)) – Resolution of the plot.

  • save (Union[str, Path, None] (default: None)) – If provided, the path where the plot will be saved.

  • kwargs – Additional arguments passed to matplotlib.pyplot.scatter() and matplotlib.pyplot.imshow().

Return type:

None

Returns:

None

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