Thanks again for working on the windows implementation of this! I've got the basic cases of ti_paga() working on my data, but when playing around with the parameters I ran into the following error when attempting to set n_dcs = 0L in ti_paga()or ti_paga_tree()
> library(dyno)
> set.seed(1)
> data <- dyntoy::generate_dataset(
+ id = "specific_example/paga",
+ num_cells = 1000,
+ num_features = 101,
+ model = "tree",
+ normalise = FALSE
+ )
>
> model_toy <- infer_trajectory(data, ti_paga(n_dcs = 0L), seed = 1)
Error: Error during trajectory inference
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/numpy/core/records.py", line 451, in __getattribute__
res = fielddict[attr][:2]
KeyError: 'X_diffmap'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/code/run.py", line 89, in <module>
sc.tl.dpt(adata, n_dcs = min(adata.obsm.X_diffmap.shape[1], 10))
File "/usr/local/lib/python3.7/site-packages/numpy/core/records.py", line 453, in __getattribute__
raise AttributeError("recarray has no attribute %s" % attr)
AttributeError: recarray has no attribute X_diffmap
It seems that there's a spot in the run.py script to skip the 'denoising' if n_dcs == 0, but then it expects there to n_dcs > 0 when it goes to calculate the pseudotime here:
Sorry for the late response. Could you update dynmethods? This will also update the ti_paga container to v0.9.9.03 next time you try to use paga. Can you confirm v0.9.9.03 solves your problem?
Thanks again for working on the windows implementation of this! I've got the basic cases of
ti_paga()
working on my data, but when playing around with the parameters I ran into the following error when attempting to setn_dcs = 0L
inti_paga()
orti_paga_tree()
It seems that there's a spot in the run.py script to skip the 'denoising' if
n_dcs == 0
, but then it expects there ton_dcs > 0
when it goes to calculate the pseudotime here:https://github.com/dynverse/ti_paga/blob/69f4771ea80f1229f768d6103bb175e5d98e4bb8/run.py#L89