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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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problem RunPAGA #225

Open JoelHaas opened 9 months ago

JoelHaas commented 9 months ago

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(

Any suggestions?

Byronxy commented 9 months ago

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?