bento.pl.density

bento.pl.density(sdata, points_key='transcripts', instance_key='cell_boundaries', kind='hist', hue=None, hue_order=None, shapes=None, hide_outside=True, axis_visible=False, frame_visible=True, title=None, dx=0.1, units='um', square=False, ax=None, shape_kws={}, fname=None, **kwargs)

Plot points as 2D density.

Parameters:

  • data (SpatialData) – Spatial formatted SpatialData object

  • kind (str, optional) – Type of density plot, by default “hist”. Options: “hist”, “kde”

  • hue (str, optional) – Variable name to color points by, by default None

  • hue_order (list, optional) – Order of hue levels, by default None

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

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

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

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

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

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

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

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

  • 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

  • shape_kws (dict, optional) – Keyword arguments for shapes, by default {}

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