sainsc.LazyKDE.plot_celltype_map

sainsc.LazyKDE.plot_celltype_map(*, remove_background=True, crop=None, scalebar=True, cmap='hls', background='black', undefined='grey', scalebar_kwargs=SCALEBAR_PARAMS, return_img=False)

Plot the cell-type annotation.

Parameters:

remove_background (bool, optional) – If True, all pixels for which sainsc.LazyKDE.background is False are set to 0.
crop (tuple[tuple[int, int], tuple[int, int]], optional) – Coordinates to crop the data defined as ((xmin, xmax), (ymin, ymax)).
scalebar (bool, optional) – If True, add a matplotlib_scalebar.scalebar.ScaleBar to the plot.
cmap (str or list or dict, optional) – If it is a string it must be the name of a cmap that can be used in seaborn.color_palette(). If it is a list of colors it must have the same length as the number of celltypes. If it is a dictionary it must be a mapping from celltpye to color. Undefined celltypes are plotted according to undefined. Colors can either be provided as string that can be converted via matplotlib.colors.to_rgb() or as (r, g, b)-tuple between 0-1.
background (str | tuple[float, float, float]) – Color for the background.
undefined (str | tuple[float, float, float]) – Color used for celltypes without a defined color.
scalebar_kwargs (dict[str, Any], optional) – Keyword arguments that are passed to matplotlib_scalebar.scalebar.ScaleBar.
return_img (bool, optional) – Return the cell-type map as 3D-array (x, y, RGB) instead of the Figure.

Return type:

Figure | ndarray[ubyte]