troutpy.pl.spatial_inout_expression

troutpy.pl.spatial_inout_expression#

troutpy.pl.spatial_inout_expression(sdata, gene, layer_cells='table', layer_extra='segmentation_free_table', spot_size_cells=7, spot_size_extra=12, extra_cmap='Aquas_contrast', cells_cmap='Pinks_contrast', title=None, save=False, figures_path='', custom_plot_filename=None)#

Plots intracellular and extracellular expression of a selected gene.

Parameters:

  • sdata – SpatialData object containing cell and extra-cellular data.

  • gene – Name of the gene to plot.

  • layer_cells (default: 'table') – Key in sdata where cell expression is stored.

  • layer_extra (default: 'segmentation_free_table') – Key in sdata where extra-cellular expression is stored.

  • spot_size_cells (default: 7) – Size of the marker for cells.

  • spot_size_extra (default: 12) – Size of the marker for extra-cellular spots.

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