aertslab/loomxpy

Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons

loomxpy's Issues

[FEATURE] A user should be able to add markers from a h5ad file

wrong address

look at this page
https://scope.aertslab.org/#/0fb6416e-d236-4837-9f24-f34ef413d801/*/welcome

SCope compatible loom files can be generated using the following packages:
R: SCopeLoomR
Python: LoomXpy or pySCENIC

the link to LoomXpy is wrong. please correct it or users can't find you.

A user should be able to read a SCope-compatible loom

It should be possible to read a SCope-compatible loom and have a LoomX object created

Allow to use pd.Series for attribute data

[BUG] Unable to add clustering

• LoomXpy version: 0.4.0
• Python version: 3.7
• Operating System: CentOS

Description

Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.

What I Did

Command:

lx.modes.rna.o.clusterings.leiden_res1 = pd.DataFrame(adata.obs["leiden_0.1"], index=adata.obs.index)

Traceback:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-38-5cf58419bb9c> in <module>
----> 1 lx.modes.rna.o.clusterings.leiden_res1 = pd.DataFrame(adata.obs["leiden_0.1"], index=adata.obs.index)

~/GitHub/LoomXpy/loomxpy/_mode.py in __setattr__(self, name, value)
    846             super().__setattr__(name, value)
    847         else:
--> 848             self.__setitem__(name=name, value=value)
    849 
    850     def __delattr__(self, name):

~/GitHub/LoomXpy/loomxpy/_mode.py in __setitem__(self, name, value)
   1541     def __setitem__(self, name: str, value: Union[pd.DataFrame, pd.Series]):
   1542         """"""
-> 1543         self.add(key=name, value=value)
   1544 
   1545     def add(

~/GitHub/LoomXpy/loomxpy/_mode.py in add(self, key, value, name, description, metadata)
   1563             description=description,
   1564             metadata=self.make_metadata(key=key, value=value, name=name)
-> 1565             if metadata is None
   1566             else metadata,
   1567         )

~/GitHub/LoomXpy/loomxpy/_mode.py in make_metadata(self, key, value, name)
   1575             reverse=False,
   1576         ):
-> 1577             _clusters.append(LoomXMetadataCluster(id=cluster_id))
   1578             super().__setattr__(
   1579                 f"cluster_{cluster_id}", LoomXMetadataCluster(id=cluster_id)

TypeError: __init__() got an unexpected keyword argument 'id'

[FEATURE] Export cluster markers

• LoomXpy version: 0.3.1
• Python version: 3.7
• Operating System: CentOS

Description

Currently the cluster markers (if any present) in the LoomX object are not exported to Loom file.

What I Did

N.A.

[BUG] Cannot read loom if markers are not present along with clustering

• LoomXpy version: 0.3.0
• Python version: 3.7
• Operating System: CentOS

Description

Reading a Loom file generated by cisTopic

What I Did

Command,

lx = read_loom(
    file_path=file_path,
    force_conversion={"annotations": True}
)

Traceback:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/lib/python3.7/site-packages/loompy/attribute_manager.py in __getattr__(self, name)
    114                 try:
--> 115                         vals = self.__dict__["storage"][name]
    116                         if vals is None:

KeyError: 'ClusterMarkers_0'

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
<ipython-input-3-e08145944dba> in <module>
      1 lx = read_loom(
      2     file_path=file_path,
----> 3     force_conversion={"annotations": True}
      4 )
~/lib/python3.7/site-packages/loomxpy/_io/_read.py in read_loom(file_path, mode_type, force_conversion)
    252                 loom_connection=loom_connection,
    253                 mode_type=_mode_type,
--> 254                 force_conversion=force_conversion,
    255             )
    256         raise Exception(f"Unable to read the loom at {file_path}")

~/lib/python3.7/site-packages/loomxpy/_io/_read.py in _read_scope_loom(loom_connection, mode_type, force_conversion)
    224     if mode_type == ModeType.RNA:
    225         return _read_scope_rna_loom(
--> 226             loom_connection=loom_connection, force_conversion=force_conversion
    227         )
    228     # Should be uncommented on production

~/lib/python3.7/site-packages/loomxpy/_io/_read.py in _read_scope_rna_loom(loom_connection, force_conversion)
    206             loom_connection=loom_connection,
    207             metadata=_metadata,
--> 208             force_conversion=force_conversion,
    209         )
    210     else:

~/lib/python3.7/site-packages/loomxpy/_io/_read.py in _read_scope_v1_rna_loom(loom_connection, metadata, force_conversion)
    167                 [
    168                     pd.DataFrame(
--> 169                         loom_connection.ra.ClusterMarkers_0,
    170                         index=loom_connection.ra.Gene,
    171                     )

~/lib/python3.7/site-packages/loompy/attribute_manager.py in __getattr__(self, name)
    121                         return vals
    122                 except KeyError:
--> 123                         raise AttributeError(f"'{type(self)}' object has no attribute '{name}'")
    124 
    125         def __setitem__(self, name: str, val: np.ndarray) -> None:

AttributeError: '<class 'loompy.attribute_manager.AttributeManager'>' object has no attribute 'ClusterMarkers_0'