bento.pl.comp

bento.pl.comp(sdata, groupby=None, group_order=None, annotate=None, adjust=True, palette=<matplotlib.colors.LinearSegmentedColormap object>, annot_color=None, sizes=(5, 30), size_norm=(10, 100), dim_order=None, legend=True, height=5, fname=None)

Plot gene composition across set of shapes. Ideally, these shapes are non-overlapping.

Parameters:

  • sdata (SpatialData) – The spatial data to be plotted.

  • groupby (str) – The column name in the data to group by.

  • group_order (list) – The order of the groups for plotting.

  • annotate (bool or list of str) – Whether to annotate the plot with gene names or a list of gene names to annotate.

  • adjust (bool) – Whether to adjust the text positions, by default True.

  • palette (str) – The color palette to use for the plot. Default is ‘red_light’.

  • annot_color (str) – The color to use for annotations. Default is None.

  • sizes (tuple) – The minimum and maximum size of the points. Default is (5, 30).

  • size_norm (tuple) – The normalization range for the point sizes. Default is (10, 100).

  • dim_order (str) – The order of the dimensions for the plot. Default is None.

  • legend (bool) – Whether to include a legend in the plot. Default is True.

  • height (int) – The height of the plot. Default is 5.

  • fname (str) – The filename to save the plot as. If None (default), the plot is not saved to file.