Is there a detailed tutorial of Lineage tree of hematopoiesis?

[hyjforesight]

Hello Dynamo, I'm wondering whether we have a detailed tutorial for plotting lineage tree of hematopoiesis (https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_megakaryocytes_appearance/tutorial_hsc_dynamo_megakaryocytes_appearance.html). Thanks! Best, YJ

I did like this.

dyn.pd.tree_model(adata, group='cell_type', progenitor='HSC', terminators=["Meg", "Ery", "Bas", 'Mon', 'Neu'], basis='umap', n_neighbors=30)
dyn.pl.state_graph(adata, group='cell_type', transition_threshold=0.001, keep_only_one_direction=True, edge_scale=1, basis='umap', color='cell_type', show_legend='on data', frontier= False,
                   save_show_or_return='show')
dyn.pl.state_graph(adata, group='cell_type', transition_threshold=0.001, keep_only_one_direction=True, edge_scale=1, basis='umap', color='cell_type', show_legend='on data', frontier= False,
                   save_show_or_return='save', save_kwargs={"prefix": 'state_graph', "ext": 'pdf', "transparent": True, "close": True, "verbose": True})

but the results look like this not

Then, I followed the example in https://dynamo-release.readthedocs.io/en/latest/_autosummary/dynamo.pd.tree_model.html#dynamo.pd.tree_model, but got errors.

dyn.pd.state_graph(adata, group='cell_type', basis='umap')
res = dyn.pd.tree_model(adata, group='cell_type', progenitor='HSC', terminators=["Meg", "Ery", "Bas", 'Mon', 'Neu'], basis='umap', n_neighbors=30)
adata.obs['cell_type2'] = adata.obs['cell_type'].copy()
adata.uns['cell_type2_graph'] = adata.uns['cell_type_graph'].copy()
adata.uns['cell_type2_graph']['group_graph'] = res
dyn.pl.state_graph(adata, group='cell_type2', transition_threshold=None, keep_only_one_direction=False, edge_scale=1, basis='umap', color='cell_type2', show_legend='on data', frontier= False,
                   save_show_or_return='show')
KeyError                                  Traceback (most recent call last)
File ~\anaconda3\envs\dynamo\lib\site-packages\pandas\core\indexes\base.py:3621, in Index.get_loc(self, key, method, tolerance)
   3620 try:
-> 3621     return self._engine.get_loc(casted_key)
   3622 except KeyError as err:

File ~\anaconda3\envs\dynamo\lib\site-packages\pandas\_libs\index.pyx:136, in pandas._libs.index.IndexEngine.get_loc()

File ~\anaconda3\envs\dynamo\lib\site-packages\pandas\_libs\index.pyx:163, in pandas._libs.index.IndexEngine.get_loc()

File pandas\_libs\hashtable_class_helper.pxi:5198, in pandas._libs.hashtable.PyObjectHashTable.get_item()

File pandas\_libs\hashtable_class_helper.pxi:5206, in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: (0, 0)

The above exception was the direct cause of the following exception:

KeyError                                  Traceback (most recent call last)
Input In [76], in <cell line: 1>()
----> 1 dyn.pl.state_graph(adata, group='cell_type2', transition_threshold=None, keep_only_one_direction=False, edge_scale=1, basis='umap', color='cell_type2', show_legend='on data', frontier= False,
      2                    save_show_or_return='show')

File ~\anaconda3\envs\dynamo\lib\site-packages\dynamo\plot\state_graph.py:241, in state_graph(adata, group, transition_threshold, keep_only_one_direction, edge_scale, state_graph, edgecolor, facecolor, graph_alpha, basis, x, y, color, layer, highlights, labels, values, theme, cmap, color_key, color_key_cmap, background, ncols, pointsize, figsize, show_legend, use_smoothed, show_arrowed_spines, ax, sort, frontier, save_show_or_return, save_kwargs, s_kwargs_dict, **kwargs)
    238 facecolor = "k" if facecolor is None else facecolor
    239 graph_alpha = 0.8 if graph_alpha is None else graph_alpha
--> 241 arrows = create_edge_patches_from_markov_chain(
    242     Pl, group_median, edgecolor=edgecolor, facecolor=facecolor, alpha=graph_alpha, tol=0.01, node_rad=15
    243 )
    244 if type(axes_list) == list:
    245     for i in range(len(axes_list)):

File ~\anaconda3\envs\dynamo\lib\site-packages\dynamo\plot\state_graph.py:54, in create_edge_patches_from_markov_chain(P, X, width, node_rad, tol, connectionstyle, facecolor, edgecolor, alpha, **kwargs)
     52 for i in range(P.shape[0]):
     53     for j in range(P.shape[0]):
---> 54         if P[i, j] > tol:
     55             if type(facecolor) == str:
     56                 fc = facecolor

File ~\anaconda3\envs\dynamo\lib\site-packages\pandas\core\frame.py:3505, in DataFrame.__getitem__(self, key)
   3503 if self.columns.nlevels > 1:
   3504     return self._getitem_multilevel(key)
-> 3505 indexer = self.columns.get_loc(key)
   3506 if is_integer(indexer):
   3507     indexer = [indexer]

File ~\anaconda3\envs\dynamo\lib\site-packages\pandas\core\indexes\base.py:3623, in Index.get_loc(self, key, method, tolerance)
   3621     return self._engine.get_loc(casted_key)
   3622 except KeyError as err:
-> 3623     raise KeyError(key) from err
   3624 except TypeError:
   3625     # If we have a listlike key, _check_indexing_error will raise
   3626     #  InvalidIndexError. Otherwise we fall through and re-raise
   3627     #  the TypeError.
   3628     self._check_indexing_error(key)

KeyError: (0, 0)

[stupidstupidstupidstupid]

I met the same question too. Have you find the fuction that is needed? Thanks in advance.

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