bento.pl.fe

bento.pl.fe(sdata, gs, instance_key='cell_boundaries', alpha=False, res=1, shapes=None, cmap=None, cbar=True, 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 spatial heatmap of flux enrichment scores.

Parameters:

  • data (SpatialData) – Spatial formatted SpatialData

  • gs (str) – Gene set name

  • res (float, optional) – Resolution of flux, by default 1

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

  • cmap (str, optional) – Colormap, by default None. If None, will use red2blue colormap.

  • cbar (bool, optional) – Whether to show colorbar, by default True

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

  • 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.

  • 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.

  • 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.