spacipy.mip_spatial

spacipy.mip_spatial(adata, uns_key='3d_spatial', color=None, highlight=None, keep_other=False, groups=None, group_col=None, order=None, group_normalize=True, ax=None, cmap=None, theme='dark', outfile=None, vmin=None, vmax=None, percentile=False, ps=1, coords_scale=0.5, angles=None, body_loc=None, rotation=None, interval=100, figsize=None, density_radius=30)

Visualization of 3d values with maximum intensity projection

Parameters:

  • adata (anndata.AnnData object) – with ‘3d_spatial’ key in adata.uns saved 3d spatial coordinates

  • color (str) – column name in adata.obs or gene name in adata.var

  • highlight (str, list) – if colored with category dtype, only highligh selected ones,

  • keep_other (bool) – weather or not keep other non-highlight groups when using highlight

  • group_col (str) – column name in adata.obs contains the batch information, if multiple groups included, the program will try to rerrange the location of each group to make sure to plot all groups in a single panel.

  • groups (str, list) – which group to use when input adata contains multiple batches

  • order (list) – order of the groups in the plot

  • group_normalize (bool) – weather or not normalize for each group when doing MIP

  • ax – ax to use

  • cmap (str|list|dict of hex color code) – color used to plot

  • theme (dark or light)

  • outfile (str) – output image name to save in local disk

  • ps (float) – point size in plot

  • coords_scale (float) – the coordinates will scaled by timing this number before mip transform