Yuanjian Huang

Hello @Xiaojieqiu, Thanks for the response. For generating `cosine_transition_matrix`, do I need to add this kwarg `other_kernels_dict={'transform': 'sqrt'}`? ```python dyn.tl.cell_velocities(adata, basis='umap', n_neighbors = 10, method='cosine', other_kernels_dict={'transform': 'sqrt'}) ``` Thanks!

thanks @Xiaojieqiu ! Appreciate it.

Hello @Xiaojieqiu, sorry for reopening this issue. I calculated the `cosine_potential` and `pearson_potential', but I believe they do not represent the real cell potential. `ddhodge_potential' looks more close to the...

Hi @Xiaojieqiu I met the same `AttributeError: 'AnchoredSizeLocator' object has no attribute 'get_subplotspec'' error like @DanieleMuraro. So I re-install dynamo by ```python git clone https://github.com/aristoteleo/dynamo-release.git cd dynamo-release/ python setup.py install...

Hello @Xiaojieqiu and @dummyindex Thanks for the response and for helping me. Sorry, I'm not professional at coding. I can just report the errors that I met. Hope it also...

check https://github.com/aristoteleo/dynamo-release/issues/392

> I am sorry but I still cannot reproduce the bug from my end. This seems like a system issue or matplotlib issue. Windows is a not a great system...

hello @stupidstupidstupidstupid, so we should add `A = A.astype(np.float32)` in the code script? ```python File ~\anaconda3\envs\dynamo\lib\site-packages\matplotlib\image.py:700, in _ImageBase.set_data(self, A) 696 self._A = cbook.safe_masked_invalid(A, copy=True) 698 if (self._A.dtype != np.uint8 and...

another issue (but I'm not sure whether it is matplotlib 3.5.1 specific): set `dyn.configuration.set_pub_style()`, tutorial can not plot figures. please check this:https://github.com/aristoteleo/dynamo-release/issues/308

I'm not sure whether this is the compatibility issue of matplotlib, but I report it here. Whatever the function is, `save_show_or_return='both'` or `save_show_or_return='all'` cannot save the plot. It only shows...