problem RunPAGA

[JoelHaas]

Hi, thanks for the great package! I am trying to run trajectory inference with the PAGA wrapper and a seurat object as described in the vignette.
when I run with my object, I get the error:

final_DC_multiK<-RunPAGA_1(srt=final_DC_multiK,group_by="final_labels", linear_reduction="PCA",nonlinear_reduction="UMAP")
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
ValueError: Data must be 1-dimensional
Run reticulate::py_last_error() for details.
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 6.3 GiB
with traceback:
── Python Exception Message ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/frame.py", line 1593, in from_dict
return cls(data, index=index, columns=columns, dtype=dtype)
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/frame.py", line 614, in init
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 464, in dict_to_mgr
return arrays_to_mgr(
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 124, in arrays_to_mgr
arrays = _homogenize(arrays, index, dtype)
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 589, in _homogenize
val = sanitize_array(
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/construction.py", line 576, in sanitize_array
subarr = _sanitize_ndim(subarr, data, dtype, index, allow_2d=allow_2d)
File "/home/jhaas/.local/share/r-miniconda/envs/SCP_env/lib/python3.8/site-packages/pandas/core/construction.py", line 627, in _sanitize_ndim
raise ValueError("Data must be 1-dimensional")
ValueError: Data must be 1-dimensional

I also get an error (a different one) with the pancreas_sub (a different one):
pancreas_sub <- RunPAGA(

• srt = pancreas_sub, group_by = "SubCellType",
  

• linear_reduction = "PCA", nonlinear_reduction = "UMAP"
  

• )
  'misc' slot is not converted.
  'tools' slot is not converted.
  Error in slot(object = object, name = "features")[[layer]] <- features :
  more elements supplied than there are to replace

Any suggestions?

[Yi Xiong]

Hi, I have the same issue when run:

pancreas_sub <- RunSCVELO(
+   srt = pancreas_sub, group_by = "SubCellType",
+   linear_reduction = "PCA", nonlinear_reduction = "UMAP"
+ )

The error is:

Error in slot(object = object, name = "features")[[layer]] <- features : 
  more elements supplied than there are to replace

Does any one have any suggestions?