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error when running infer_trajectory with paga_tree method and umap embedding_type #2

Open lixin4306ren opened 5 years ago

lixin4306ren commented 5 years ago

It works for embedding_type="fa" but not umap. 

Error: Error during trajectory inference 
Traceback (most recent call last):
  File "/code/run.py", line 117, in <module>
    dimred = pd.DataFrame([x for x in adata.obsm['X_umap'].T]).T
  File "/usr/local/lib/python3.7/site-packages/numpy/core/records.py", line 506, in __getitem__
    obj = super(recarray, self).__getitem__(indx)
ValueError: no field of name X_umap
rcannood commented 5 years ago

Please update dynmethods:

devtools::install_github("dynverse/dynmethods")

Does this solve your problem?

lixin4306ren commented 5 years ago

No, I think I have already had the latest dynmethods installed.

the command I used:

model_paga_tree_umap <- infer_trajectory(nor_merge_dataset,ti_paga_tree(embedding_type="umap"),verbose=T,return_verbose=T,n_top_genes=2000)

full running information:

Executing 'paga_tree' on 'nor_subset'
With parameters: list(n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L,     embedding_type = "umap", n_top_genes = 2000),
inputs: counts, and
priors : start_id
Input saved to /tmp/folders/wn/5wyp_69d36b50ypsrc8w5nn40000gn/T//Rtmpjoefwr/file1250e2f279a8d/ti
Running method using babelwhale
Running /usr/local/bin/docker run -e 'TMPDIR=/tmp2' --workdir /ti/workspace -v \
  '/tmp/folders/wn/5wyp_69d36b50ypsrc8w5nn40000gn/T//Rtmpjoefwr/file1250e2f279a8d/ti:/ti' -v \
  '/tmp/folders/wn/5wyp_69d36b50ypsrc8w5nn40000gn/T//Rtmpjoefwr/file1250e5113b72a/tmp:/tmp2' \
  'dynverse/ti_paga_tree:v0.9.9.03' --dataset /ti/input.h5 --output /ti/output.h5 --use_priors all
Traceback (most recent call last):
  File "/code/run.py", line 117, in <module>
    dimred = pd.DataFrame([x for x in adata.obsm['X_umap'].T]).T
  File "/usr/local/lib/python3.7/site-packages/numpy/core/records.py", line 506, in __getitem__
    obj = super(recarray, self).__getitem__(indx)
ValueError: no field of name X_umap
Messages (not in order):
Error: Error during trajectory inference 
Traceback (most recent call last):
  File "/code/run.py", line 117, in <module>
    dimred = pd.DataFrame([x for x in adata.obsm['X_umap'].T]).T
  File "/usr/local/lib/python3.7/site-packages/numpy/core/records.py", line 506, in __getitem__
    obj = super(recarray, self).__getitem__(indx)
ValueError: no field of name X_umap
zouter commented 5 years ago

I have a hard time reproducing this, I'm running the following with the latest version of paga tree:

library(dyno)

dataset <- dyntoy::generate_dataset(num_cells = 1000, num_features = 100)
trajectory <- infer_trajectory(dataset, "dynverse/ti_paga_tree:v0.9.9.05", embedding_type = "umap", n_top_genes = 2000)

And it works. Could you try the same with dynverse/ti_paga_tree:v0.9.9.05 @lixin4306ren ? This new version will be pushed to dynmethods soon once all methods finish building.

Thanks!

zouter commented 5 years ago

New version is now in dynverse/dynmethods master.

rcannood commented 5 years ago

@lixin4306ren Can you confirm whether reinstalling dynmethods fixes your problem?