Label Transfer Using the SCVI-tools

[aydinbol]

Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried doing the label transfer using the SCVI-tools as you demonstrated here: https://kzhang.org/SnapATAC2/tutorials/annotation.html

The RNA-seq data I'm using is from the same disease model, but the cells are not overlapping at all.
It looks like this:

Do you have any suggestions to improve the label transferring?
Do you have any plans of adding the FindTransferAnchors function from the Seurat package or do you think it is a better approach?

Thank you.

[yojetsharma]

Hi, I am facing issue at an earlier stage of the tutorial itself:
I have merged 3 atac-seq samples (from a multiome exp) and carried out the initial steps as per the standard tutorial. I use the snRNA of these samples processed using scanpy to annotate the clusters in the ATAC seq dataset. However, I am not able to understand how to proceed. Because when I do exactly as per the tutorial i get the following:

>>> vae.train(max_epochs=1000, early_stopping=True)
/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/cuda/__init__.py:619: UserWarning: Can't initialize NVML
  warnings.warn("Can't initialize NVML")
/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/cuda/__init__.py:749: UserWarning: CUDA initialization: The NVIDIA driver on your system is too old (found version 9020). Please update your GPU driver by downloading and installing a new version from the URL: http://www.nvidia.com/Download/index.aspx Alternatively, go to: https://pytorch.org to install a PyTorch version that has been compiled with your version of the CUDA driver. (Triggered internally at ../c10/cuda/CUDAFunctions.cpp:108.)
  return torch._C._cuda_getDeviceCount() if nvml_count < 0 else nvml_count
INFO: GPU available: False, used: False
2024-08-26 00:23:29 - INFO - GPU available: False, used: False
INFO: TPU available: False, using: 0 TPU cores
2024-08-26 00:23:29 - INFO - TPU available: False, using: 0 TPU cores
INFO: IPU available: False, using: 0 IPUs
2024-08-26 00:23:29 - INFO - IPU available: False, using: 0 IPUs
INFO: HPU available: False, using: 0 HPUs
2024-08-26 00:23:29 - INFO - HPU available: False, using: 0 HPUs
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/scvi/model/base/_training_mixin.py", line 143, in train
    return runner()
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/scvi/train/_trainrunner.py", line 98, in __call__
    self.trainer.fit(self.training_plan, self.data_splitter)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/scvi/train/_trainer.py", line 220, in fit
    super().fit(*args, **kwargs)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/lightning/pytorch/trainer/trainer.py", line 538, in fit
    model = _maybe_unwrap_optimized(model)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/lightning/pytorch/utilities/compile.py", line 125, in _maybe_unwrap_optimized
    from torch._dynamo import OptimizedModule
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/__init__.py", line 64, in <module>
    torch.manual_seed = disable(torch.manual_seed)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/decorators.py", line 50, in disable
    return DisableContext()(fn)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/eval_frame.py", line 410, in __call__
    (filename is None or trace_rules.check(fn))
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 3378, in check
    return check_verbose(obj, is_inlined_call).skipped
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 3361, in check_verbose
    rule = torch._dynamo.trace_rules.lookup_inner(
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 3442, in lookup_inner
    rule = get_torch_obj_rule_map().get(obj, None)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 2782, in get_torch_obj_rule_map
    obj = load_object(k)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 2807, in load_object
    obj = _load_obj_from_str(x[0])
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_dynamo/trace_rules.py", line 2795, in _load_obj_from_str
    return getattr(importlib.import_module(module), obj_name)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/distributed/_tensor/__init__.py", line 6, in <module>
    import torch.distributed._tensor.ops
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/distributed/_tensor/ops/__init__.py", line 2, in <module>
    from .embedding_ops import *  # noqa: F403
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/distributed/_tensor/ops/embedding_ops.py", line 8, in <module>
    import torch.distributed._functional_collectives as funcol
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/distributed/_functional_collectives.py", line 920, in <module>
    _register_ops()
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/distributed/_functional_collectives.py", line 911, in _register_ops
    impl_abstract(f"c10d_functional::{op_name}")(meta_impl)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_custom_ops.py", line 253, in impl_abstract
    return torch.library.impl_abstract(qualname, func, _stacklevel=2)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/library.py", line 448, in impl_abstract
    source = torch._library.utils.get_source(_stacklevel + 1)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/_library/utils.py", line 39, in get_source
    frame = inspect.getframeinfo(sys._getframe(stacklevel))
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 1629, in getframeinfo
    lines, lnum = findsource(frame)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 952, in findsource
    module = getmodule(object, file)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 875, in getmodule
    f = getabsfile(module)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 844, in getabsfile
    _filename = getsourcefile(object) or getfile(object)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 817, in getsourcefile
    filename = getfile(object)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/site-packages/torch/package/package_importer.py", line 698, in _patched_getfile
    return _orig_getfile(object)
  File "/home/praghu/yojetsharma/.conda/envs/signac/lib/python3.10/inspect.py", line 778, in getfile
    raise TypeError('{!r} is a built-in module'.format(object))
TypeError: <module '' from '/ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/snapatac2test'> is a built-in module