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The plot of RNA velocity has no arrows

Open zcaiwei opened this issue 1 year ago • 5 comments

Hi, I'm having another problem when plotting RNA velocity. The following is my command:

cellDancer_df=cd.compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gene', expression_scale='power10', projection_neighbor_size=5, speed_up=(100,100))
fig, ax = plt.subplots(figsize=(10,10))
cdplt.scatter_cell(ax,
                   cellDancer_df,
                   colors=color_dict,
                   alpha=0.5,
                   s=30,
                   velocity=True,
                   legend='on',
                   min_mass=15,
                   arrow_grid=(20,20),
                   )
ax.axis('off')
plt.show()

This is my plot of RNA velocity: RNA_velocity_without_arrows We can see the plot has no arrows. So I checked the velocity1 values of cellDancer_df, and I found some data rows(3268 rows × 17 columns) have values, the following are my data without NaN: nonan_plot

Can you tell me how to adjust the parameters to get the arrows in the RNA velocity plot?

zcaiwei avatar Dec 22 '23 07:12 zcaiwei