troutpy.pl.coupled_scatter

troutpy.pl.coupled_scatter#

troutpy.pl.coupled_scatter(sdata, layer='extracellular_transcripts', output_path='', transcript_group='distance_to_source_cell', save=True, format='pdf', xcoord='x', ycoord='y', xcellcoord='x_centroid', ycellcoord='y_centroid', colormap='Blues', size=2, color_cells='red', figsize=(10, 7), vmax=None)#

Plots a scatter plot of transcript locations and cell centroids, coloring the transcripts by a specific feature (e.g., distance to the closest cell) and optionally saving the plot to a file.

Parameters:

  • sdata (spatialdata.SpatialData) – A spatial data object that contains transcript and cell information.

  • layer (str) – The key for the layer in sdata.points that contains transcript data (default: ‘extracellular_transcripts’).

  • output_path (str) – The directory path where the plot will be saved. If not provided, the plot will not be saved (default: ‘’).

  • transcript_group (str) – The key in the transcript data (e.g., distance to the source cell) to be used for coloring the scatter plot (default: ‘distance_to_source_cell’).

  • save (bool) – Whether to save the plot to a file. If True, the plot is saved to output_path (default: True).

  • format (str) – The format for saving the plot (e.g., ‘pdf’, ‘png’). This is only used if save=True (default: ‘pdf’).

  • xcoord (str) – The column name in the transcript data representing the x-coordinate (default: ‘x’).

  • ycoord (str) – The column name in the transcript data representing the y-coordinate (default: ‘y’).

  • xcellcoord (str) – The column name in the cell data representing the x-coordinate of cell centroids (default: ‘x_centroid’).

  • ycellcoord (str) – The column name in the cell data representing the y-coordinate of cell centroids (default: ‘y_centroid’).

  • colormap (str) – The colormap to use for coloring the transcripts based on the transcript_group values (default: ‘Blues’).

  • size (float) – The size of the scatter points for cells and transcripts. Transcripts are scaled down by 0.1 (default: 2).

  • color_cells (str) – The color to use for the cell centroids (default: ‘red’).

  • figsize (tuple) – The size of the figure in inches (width, height). This controls the dimensions of the plot (default: (10, 7)).

  • vmax (float) – The upper limit for the colormap. If provided, this limits the color scale to values below vmax (default: None).

Returns:

None

Notes

  • The transcript data and cell centroid data are extracted from sdata.

  • The vmax parameter allows control over the maximum value of the color scale for better visualization control.

  • The plot is saved in the specified format and at the specified output path if save=True.

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