snap.annotate error

[mw-neuro]

Hi, thank you for the amazing resource!

I'm getting the below error that I cannot find a solution for when running the following code:

snap.annotate(
adata,
marker_genes,
group_name="leiden",
layer="scvi_normalized",
)

Any help on how to fix this error would be appreciated!

---

TypeError Traceback (most recent call last)
Cell In[41], [line 1]
----> [1]snap.annotate(
[2] adata,
[3] marker_genes,
[4] group_name="leiden",
[5] layer="scvi_normalized",
[6] )

File ~/.local/lib/python3.10/site-packages/hnoca/snapseed/annotate.py:113, in annotate(adata, marker_dict, group_name, layer, **kwargs)
93 def annotate(
94 adata: ad.AnnData,
95 marker_dict: dict,
(...)
98 **kwargs
99 ) -> pd.DataFrame:
100 """
101 Annotate clusters based on a manually defined cell type markers.
102
(...)
111 pd.DataFrame with assignments
112 """
--> 113 assignments = annotate_snap(adata, marker_dict, group_name, layer=layer, **kwargs)
114 # Join cluster-level results with adata
...
282 if self._list_type is None:
--> 283 raise TypeError("invalid operation on untyped list")
284 return self._list_type

TypeError: invalid operation on untyped list

[yliu38]

Hello,

Thanks for the excellent work!
But I also encounter the similar issue. I covert my seurat object to h5ad file and read in python. Also, I added the lognorm layer through
adata.layers["lognorm"] = np.log1p(adata.X).

and then run the snapseed annotations like below:

Annotate anndata objects

snap.annotate(
adata,
marker_genes,
group_name="seurat_clusters",
layer="lognorm",
)
TypeError Traceback (most recent call last)
Cell In[10], line 2
1 # Annotate anndata objects
----> 2 snap.annotate(
3 adata,
4 marker_genes,
5 group_name="seurat_clusters",
6 layer="lognorm",
7 )

File ~\AppData\Local\anaconda3\Lib\site-packages\snapseed\annotate.py:122, in annotate(adata, marker_dict, group_name, method, layer, **kwargs)
102 """
103 Annotate clusters based on a manually defined cell type markers.
104
(...)
118 Additional arguments to pass to the annotation function.
119 """
121 if method == "auroc":
--> 122 assignments = annotate_snap(
123 adata, marker_dict, group_name, layer=layer, **kwargs
124 )
125 elif method == "trinatize":
126 assignments = annotate_cytograph(
127 adata, marker_dict, group_name, layer=layer, **kwargs
128 )

File ~\AppData\Local\anaconda3\Lib\site-packages\snapseed\auroc.py:57, in annotate_snap(adata, marker_dict, group_name, layer, auc_weight, expr_weight, marker_summary_fun, apply_fun)
55 # Compute AUROC and fraction nonzero for marker features
56 features = marker_mat.columns
---> 57 metrics = auc_expr(
58 adata, group_name, features=features, layer=layer, apply_fun=apply_fun
59 )
61 marker_mat = marker_mat.loc[:, metrics["features"]]
62 if marker_summary_fun == "max":

File ~\AppData\Local\anaconda3\Lib\site-packages\snapseed\auroc.py:111, in auc_expr(adata, group_name, features, layer, compute_auroc, compute_frac_nonzero, compute_frac_nonzero_out, apply_fun)
109 # Compute AUROC and fraction nonzero
110 groups = jnp.array(le.transform(adata.obs[group_name]))
--> 111 expr, features = get_expr(adata, features=features, layer=layer)
112 auroc, frac_nonzero, frac_nonzero_out = expr_auroc_over_groups(
113 expr,
114 groups,
(...)
118 apply_fun=apply_fun,
119 )
121 return dict(
122 frac_nonzero=frac_nonzero,
123 frac_nonzero_out=frac_nonzero_out,
(...)
126 groups=le.classes_,
127 )

File ~\AppData\Local\anaconda3\Lib\site-packages\snapseed\utils.py:65, in get_expr(adata, features, layer)
60 if features is not None:
61 # intersect with adata features
62 features = list(set(features) & set(adata.var_names))
63 adata = adata[
64 :,
---> 65 match(
66 numba.typed.List(features), numba.typed.List(adata.var_names.tolist())
67 ),
68 ]
69 else:
70 features = adata.var_names.copy().tolist()

File ~\AppData\Local\anaconda3\Lib\site-packages\numba\core\dispatcher.py:733, in _DispatcherBase.typeof_pyval(self, val)
730 # Not going through the resolve_argument_type() indirection
731 # can save a couple µs.
732 try:
--> 733 tp = typeof(val, Purpose.argument)
734 except ValueError:
735 tp = types.pyobject

File ~\AppData\Local\anaconda3\Lib\site-packages\numba\core\typing\typeof.py:33, in typeof(val, purpose)
31 # Note the behaviour for Purpose.argument must match _typeof.c.
32 c = _TypeofContext(purpose)
---> 33 ty = typeof_impl(val, c)
34 if ty is None:
35 msg = _termcolor.errmsg(
36 f"Cannot determine Numba type of {type(val)}")

File ~\AppData\Local\anaconda3\Lib\functools.py:909, in singledispatch..wrapper(*args, **kw)
905 if not args:
906 raise TypeError(f'{funcname} requires at least '
907 '1 positional argument')
--> 909 return dispatch(args[0].class)(*args, **kw)

File ~\AppData\Local\anaconda3\Lib\site-packages\numba\core\typing\typeof.py:50, in typeof_impl(val, c)
47 if tp is not None:
48 return tp
---> 50 tp = getattr(val, "numba_type", None)
51 if tp is not None:
52 return tp

File ~\AppData\Local\anaconda3\Lib\site-packages\numba\typed\typedlist.py:283, in List.numba_type(self)
280 @Property
281 def numba_type(self):
282 if self._list_type is None:
--> 283 raise TypeError("invalid operation on untyped list")
284 return self._list_type

TypeError: invalid operation on untyped list

Could you please help with this when you get the time? Many thanks!

[yliu38]

Hi, thank you for the amazing resource!

I'm getting the below error that I cannot find a solution for when running the following code:

snap.annotate( adata, marker_genes, group_name="leiden", layer="scvi_normalized", )

Any help on how to fix this error would be appreciated!

TypeError Traceback (most recent call last) Cell In[41], [line 1] ----> [1]snap.annotate( [2] adata, [3] marker_genes, [4] group_name="leiden", [5] layer="scvi_normalized", [6] )

File ~/.local/lib/python3.10/site-packages/hnoca/snapseed/annotate.py:113, in annotate(adata, marker_dict, group_name, layer, **kwargs) 93 def annotate( 94 adata: ad.AnnData, 95 marker_dict: dict, (...) 98 **kwargs 99 ) -> pd.DataFrame: 100 """ 101 Annotate clusters based on a manually defined cell type markers. 102 (...) 111 pd.DataFrame with assignments 112 """ --> 113 assignments = annotate_snap(adata, marker_dict, group_name, layer=layer, **kwargs) 114 # Join cluster-level results with adata ... 282 if self._list_type is None: --> 283 raise TypeError("invalid operation on untyped list") 284 return self._list_type

TypeError: invalid operation on untyped list

Hi! Do you find a way to solve this? Many thanks!

[Marius1311]

Hi @yliu38, please update to v0.2.1 and check whether the error persists.