dyn.tl.cell_velocities() does not work when dyn.tl.dynamics is run with a group parameter #716
Unanswered
GriffinBINF
asked this question in
Q&A
Replies: 0 comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Hi Dynamo team,
I am working with a dataset that is naturally subsetted into different kinetic regimes based on the timepoint at which the sample was taken, so I thought it would be best to use those subsets as a grouping.
dyn.tl.dynamics(
adata,
use_smoothed=True,
assumption_mRNA='kinetic',
model='deterministic',
re_smooth = True,
tkey='time_numeric',
filter_gene_mode = 'no',
group='Timepoint',
cores = 20
)
tl.dynamics appears to run fine as long as I dont use the stochastic model, however the output adata stores separate vel_params for each timepoint. This causes an issue with dyn.tl.cell_velocities with KeyError: 'The key of velocity related parameters are not found in varm.' This error persists even if I specify one of the grouped vel_params.
Please let me know if there are any quick fixes or troubleshooting steps I could do.
Cheers,
Griffin
Beta Was this translation helpful? Give feedback.
All reactions