Garfield.plot.plot_multi_patterns_spatial

Garfield.plot.plot_multi_patterns_spatial(adata, topic_prop, basis='spatial', bw=False, img=None, library_id=_empty, crop_coord=None, img_key=_empty, spot_size=None, na_color=None, scale_factor=None, scale_default=0.5, show_img=True, display_zeros=False, figsize=(10, 10), **kwargs)

Plot taken from cell2location at https://github.com/BayraktarLab/cell2location. Able to display zeros and also on umap through the basis function

Args:

adata (_type_): Adata object with spatial coordinates in adata.obsm[‘spatial’] topic_prop (_type_): Topic proportion obtained from STAMP. basis (str, optional): Which basis to plot in adata.obsm. Defaults to “spatial”. bw (bool, optional): Defaults to False. img (_type_, optional): . Defaults to None. library_id (_type_, optional): _description_. Defaults to _empty. crop_coord (_type_, optional): _description_. Defaults to None. img_key (_type_, optional): _description_. Defaults to _empty. spot_size (_type_, optional): _description_. Defaults to None. na_color (_type_, optional): _description_. Defaults to None. scale_factor (_type_, optional): _description_. Defaults to None. scale_default (float, optional): _description_. Defaults to 0.5. show_img (bool, optional): Whether to display spatial image. Sets to false automatically when displaying umap. Defaults to True. display_zeros (bool, optional): Whether to display cells that have low counts values to grey colour. Defaults to False. figsize (tuple, optional): Figsize of image. Defaults to (10, 10).

Returns:

_type_: Function taken from cell2location at https://cell2location.readthedocs.io/en/latest/_modules/cell2location/plt/plot_spatial.html#plot_spatial. Able to plot both on spatial and umap coordinates. Still very raw.