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)#

The function plots arrows from source to target cells based on transcript proximity, color-coding source and target cells, and transcript locations. An optional image layer can be overlaid behind the plot.

Parameters:

  • sdata (spatialdata.SpatialData) – The AnnData object containing the spatial omics data.

  • layer (str) – The key in sdata for the extracellular transcript layer to analyze. Default is ‘extracellular_transcripts_enriched’.

  • gene (str) – The gene of interest. Default is ‘Arc’.

  • gene_key (str) – The key for gene names in the data. Default is ‘feature_name’.

  • cell_id_key (str) – The key for cell IDs. Default is ‘cell_id’.

  • color_target (str) – Color for the target cells. Default is ‘blue’.

  • color_source (str) – Color for the source cells. Default is ‘red’.

  • color_transcript (str) – Color for the transcript locations. Default is ‘green’.

  • spatial_key (str) – The key for spatial coordinates in sdata. Default is ‘spatial’.

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

  • img_alpha (float) – Transparency level for the background image. Default is None (no image).

  • image_cmap (str) – Colormap for the image. Default is None.

  • size (float) – Size of the plotted points (cells and transcripts). Default is 8.

  • alpha (float) – Transparency level for plotted points. Default is 0.6.

  • title (str) – Title of the plot. Default is the gene name.

  • legend_loc (str) – Location of the legend on the plot. Default is ‘best’.

  • figsize (tuple) – Size of the plot. Default is (10, 10).

  • dpi (int) – Resolution of the plot. Default is 100.

  • save (str) – If provided, the path where the plot will be saved.

  • kwargs – Additional arguments passed to the scatter and imshow functions for customization.

Returns:

None The function displays or saves a plot of interactions between cells and transcripts.

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