bento.pl.shapes

bento.pl.shapes(sdata, shapes=None, color=None, color_style='outline', hide_outside=True, dx=0.1, units='um', axis_visible=False, frame_visible=True, title=None, square=False, ax=None, fname=None, **kwargs)

Plot shape layers.

Parameters:

  • data (SpatialData) – Spatial formatted SpatialData

  • shapes (list, optional) – List of shapes to plot, by default None. If None, will plot cell and nucleus shapes by default.

  • color (str, optional) – Color name, by default None. If None, will use default theme color.

  • color_style (“outline” or “fill”) – Whether to color the outline or fill of the shape, by default “outline”.

  • hide_outside (bool, optional) – Whether to hide molecules outside of cells, by default True.

  • dx (float, optional) – Size of scalebar in units, by default 0.1.

  • units (str, optional) – Units of scalebar, by default “um”.

  • axis_visible (bool, optional) – Whether to show axis, by default False.

  • frame_visible (bool, optional) – Whether to show frame, by default True.

  • title (str, optional) – Title of plot, by default None.

  • square (bool, optional) – Whether to make axis square, by default False.

  • ax (matplotlib.axes.Axes, optional) – Axis to plot on, by default None. If None, will use current axis.

  • sync_shapes (bool, optional) – Whether to synchronize shapes with points, by default True.

  • fname (str, optional) – Filename to save figure to, by default None. If None, will not save figure.