sainsc.lazykde.LazyKDE.plot_KDE

sainsc.lazykde.LazyKDE.plot_KDE(*, gene=None, remove_background=False, crop=None, scalebar=True, im_kwargs=dict(), scalebar_kwargs=SCALEBAR_PARAMS)

Plot the kernel density estimate (KDE).

By default this will plot the KDE of the total mRNA (sainsc.LazyKDE.total_mRNA_KDE). If gene is specified the respective KDE will be computed and plotted.

Parameters:

gene (str, optional) – Gene in sainsc.LazyKDE.genes to use for plotting.
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.
im_kwargs (dict[str, Any], optional) – Keyword arguments that are passed to matplotlib.pyplot.imshow().
scalebar_kwargs (dict[str, Any], optional) – Keyword arguments that are passed to matplotlib_scalebar.scalebar.ScaleBar.

Return type:

Figure

Raises:

ValueError – If sainsc.LazyKDE.total_mRNA_KDE has not been calculated.