Problems with figures generated by scv.pl.velocity_graph(adata)

[ETAOIK]

Hi, I am new to scVelo application and I have some problems during studying the tutorial 'Velocity graph and pseudotime' in https://scvelo.readthedocs.io/en/stable/VelocityBasics/,
In my output, cell-to-cell transitions didn't overlap with the umap clusters plot like following(Fig.1),
scv.pl.velocity_graph(adata,threshold=0.2)

only set arrows=True could made it like the following(Fig.2), and in this situation edges_on_top=None didn't works

also, the the velocity graph generated by scv.pl.velocity_graph(adata) is quite small and the legend is quite big(Fig.3)

x, y = scv.utils.get_cell_transitions(adata, basis='umap', starting_cell=70)
ax = scv.pl.velocity_graph(adata, c='lightgrey', edge_width=.05, show=False)
ax = scv.pl.scatter(adata, x=x, y=y, s=120, c='ascending', cmap='gnuplot', ax=ax)

My question is how to deal with it. Any help is greatly appreciated!

[joe-jhou2]

I run into the same problem. Try to modify some parameter, but nothing changed.

[ETAOIK]

I modified the source codes, and found one solution, although it didn't solve the problems fundamentally (cause if you didn't set arrows=True, the changes would not work), so here is my solution:
modify the codes of /scvelo-master/scvelo/plotting/velocity_graph like following (Line 83)

1. change the zorder from 0 to 2 (let the zorder bigger than that of edges) first,
2. and then add fontsize and figsize parameters statements (Set according to your needs):

Before changed:
ax = scatter(adata, layer=layer, color=color, size=size, ax=ax, zorder=0, **kwargs)
After changed:
ax = scatter(adata, layer=layer, color=color, size=size, ax=ax, zorder=2, fontsize=10,figsize=(8,6), **kwargs)

velocity graph and transition plot before changes:

velocity graph and transition plot after changes:

the following plot should add one more zorder statement (zorder=3)
x, y = scv.utils.get_cell_transitions(adata, basis='umap', starting_cell=70)
ax = modified_velocity_graph(adata, arrows=True, c='lightgrey', edge_width=.05, show=False)
ax = scv.pl.scatter(adata, x=x, y=y, s=120, c='ascending', cmap='gnuplot', ax=ax, zorder=3)

Although this solution could generate the correct figures, it only works in the situation of setting arrows=True, setting arrows=False will still lead to the wrong layer overlapping. And I would like to mention, setting arrows=True will cost more time (more computing power is cost in the process of computing directed graph?). I don't know how to correct it fundamentally, but at least now, we have the correct output figures. Hope it would be solved fundamentally asap. Thanks all