Issue when conducting CCI analysis using human DB

[CenFWNW]

Hi,

Thank you for creating this great tool! I have been working on serial CosMx data 3D reconstruction and it worked really well. There is an issue encountered when I was trying to conduct CCI analysis on the re-constructed data set, here is my issue:

First, I saved my aligned cell coordinates to the adata.obsm['aligned_spatial_3D'], they look like:

I then followed the tutorial to find neighbor by using the following codes:

_, aligned_adata = st.tl.neighbors(
aligned_adata,
basis='spatial',
spatial_key='aligned_spatial_3D',
n_neighbors=20
)

The first issue happened here is 'distances' and 'connectivities' slot was not created by the function, what I did was:
aligned_adata.obsp['distances'] = aligned_adata.obsp['spatial_distances']
aligned_adata.obsp['connectivities'] = aligned_adata.obsp['spatial_connectivities']

Then the plot_connections function worked fine:
st.pl.plot_connections(
aligned_adata,
cat_key='cell_type',
save_show_or_return='show'
)

next by following the tutorial, I ran:
sender_ct = 'Epithelial_1'
receptor_ct = 'Epithelial_2'

st.tl.prepare_cci_cellpair_adata(aligned_adata, sender_group=sender_ct,
receiver_group=receptor_ct, group='cell_type', all_cell_pair=True)

res = st.tl.find_cci_two_group(aligned_adata,
path="~/",
species='human',
group='cell_type',
sender_group=sender_ct,
receiver_group=receptor_ct,
#lr_pair=None,
filter_lr='inner',
min_pairs=0,
min_pairs_ratio=0,
top=20,)

Here returns an wired error:

---

KeyError Traceback (most recent call last)
Cell In[79], line 1
----> 1 res = st.tl.find_cci_two_group(aligned_adata,
2 path="~/",
3 species='human',
4 group='cell_type',
5 sender_group=sender_ct,
6 receiver_group=receptor_ct,
7 #lr_pair=None,
8 filter_lr='inner',
9 min_pairs=0,
10 min_pairs_ratio=0,
11 top=20,)

File ~/.local/lib/python3.11/site-packages/spateo/configuration.py:204, in SpateoAdataKeyManager.check_adata_is_type..decorator..wrapper(*args, **kwargs)
202 else:
203 raise ConfigurationError(f"AnnData is not AnnData object, but {type(adata)}.")
--> 204 return func(*args, **kwargs)

File ~/.local/lib/python3.11/site-packages/spateo/tools/cci_two_cluster.py:241, in find_cci_two_group(adata, path, species, layer, group, lr_pair, sender_group, receiver_group, mode, filter_lr, top, spatial_neighbors, spatial_distances, min_cells_by_counts, min_pairs, min_pairs_ratio, num, pvalue, fdr)
180 ligands = [
181 l
182 for l in ligands_test
(...)
237 ]
238 ]
240 # ligand_sender_spec
--> 241 adata_l = adata[:, ligands]
242 for g in adata.obs[group_sp].unique():
243 # Of all cells expressing particular ligand, what proportion are group g:
244 frac = (adata_l[adata_l.obs[group_sp] == g].X > 0).sum(axis=0) / (adata_l.X > 0).sum(axis=0)

File ~/.local/lib/python3.11/site-packages/anndata/_core/anndata.py:1085, in AnnData.getitem(self, index)
1083 def getitem(self, index: Index) -> AnnData:
1084 """Returns a sliced view of the object."""
-> 1085 oidx, vidx = self._normalize_indices(index)
1086 return AnnData(self, oidx=oidx, vidx=vidx, asview=True)

File ~/.local/lib/python3.11/site-packages/anndata/_core/anndata.py:1066, in AnnData._normalize_indices(self, index)
1065 def _normalize_indices(self, index: Index | None) -> tuple[slice, slice]:
-> 1066 return _normalize_indices(index, self.obs_names, self.var_names)

File ~/.local/lib/python3.11/site-packages/anndata/_core/index.py:36, in _normalize_indices(index, names0, names1)
34 ax0, ax1 = unpack_index(index)
35 ax0 = _normalize_index(ax0, names0)
---> 36 ax1 = _normalize_index(ax1, names1)
37 return ax0, ax1

File ~/.local/lib/python3.11/site-packages/anndata/_core/index.py:100, in _normalize_index(indexer, index)
98 if np.any(positions < 0):
99 not_found = indexer[positions < 0]
--> 100 raise KeyError(
101 f"Values {list(not_found)}, from {list(indexer)}, "
102 "are not valid obs/ var names or indices."
103 )
104 return positions # np.ndarray[int]
105 else:

KeyError: "Values ['Efna4', 'Tgfb2', 'Egf', 'Il20', 'Ccl5', 'Csf2', 'Tnfsf9', 'Il17b', 'Pdgfb', 'Vegfa', 'Wnt5b', 'Ccl2', 'Ccl28', 'Csf3', 'Angptl1', 'Igf2', 'Wnt7b', 'Il15', 'Il1a', 'Il17a', 'Klk3', 'Ccl13', 'Areg', 'Cxcl16', 'Vegfc', 'Ccl21', 'Efnb2', 'Col1a1', 'Il12a', 'Selplg', 'Tnfsf13b', 'Tnfsf12', 'Wnt7a', 'Col9a3', 'Inha', 'Fgf9', 'Gdf15', 'Pgf', 'Thbs1', 'Pecam1', 'Col4a1', 'Il33', 'Ccl19', 'Col9a2', 'Cxcl12', 'Thbs2', 'Cd274', 'Bmp4', 'Mif', 'Inhba', 'Csf1', 'Spp1', 'Il23a', 'Dll1', 'Tnfsf10', 'Vtn', 'Il18', 'Cd70', 'Ifng', 'Cd209', 'Ccl8', 'Tnf', 'Pdgfa', 'Wnt3', 'Il1b', 'Jag1', 'Ltb', 'Cxcl8', 'Il7', 'Lif', 'Col6a3', 'Cdh1', 'Itgb2', 'Itgb1', 'Efna1', 'Efnb1', 'Bmp7', 'Cdh5', 'Fgf2', 'Angpt2', 'Hla-dqa1', 'Il10', 'Ptprc', 'Tgfb3', 'Il6', 'Wnt9a', 'Ccl18', 'Cxcl9', 'Anxa1', 'Il12b', 'Vegfd', 'Cd86', 'Rarres2', 'Ins', 'Fgf1', 'Clcf1', 'Osm', 'Cxcl10', 'Nppc', 'Cxcl5', 'Clec2b', 'Sell', 'App', 'Il2', 'Fgf7', 'Inhbb', 'Clec2d', 'Tgfb1', 'Adgre5', 'Esam', 'Angpt1', 'Il16', 'Hla-dpa1', 'Cx3cl1', 'Col1a2', 'Hla-dpb1', 'Ccl15', 'Fgf18', 'Nrg1', 'Ccl11', 'Efna5', 'Bmp2', 'Cd80', 'Il24', 'Kitlg', 'Faslg', 'Gas6', 'Vegfb', 'Col4a5', 'Icam2', 'Hgf', 'Itga9', 'Bmp5', 'Igf1', 'Lgals9', 'Il36g', 'Hla-dra', 'Il34', 'Pdgfc', 'Vwf', 'Tnfsf4', 'Wnt5a', 'Tnfsf14', 'Pdgfd', 'Icoslg', 'Wnt10b', 'Col6a2', 'Icam1', 'Col6a1', 'Dll4', 'Cd69', 'Pdcd1lg2', 'Col4a2', 'Wnt11', 'Fn1', 'Cd40lg', 'Il11'], from ['Efna4', 'Tgfb2', 'Egf', 'Il20', 'Ccl5', 'Csf2', 'Tnfsf9', 'Il17b', 'Pdgfb', 'Vegfa', 'Wnt5b', 'Ccl2', 'Ccl28', 'Csf3', 'Angptl1', 'Igf2', 'Wnt7b', 'Il15', 'Il1a', 'Il17a', 'Klk3', 'Ccl13', 'Areg', 'Cxcl16', 'Vegfc', 'Ccl21', 'Efnb2', 'Col1a1', 'Il12a', 'Selplg', 'Tnfsf13b', 'Tnfsf12', 'Wnt7a', 'Col9a3', 'Inha', 'Fgf9', 'Gdf15', 'Pgf', 'Thbs1', 'Pecam1', 'Col4a1', 'Il33', 'Ccl19', 'Col9a2', 'Cxcl12', 'Thbs2', 'Cd274', 'Bmp4', 'Mif', 'Inhba', 'Csf1', 'Spp1', 'Il23a', 'Dll1', 'Tnfsf10', 'Vtn', 'Il18', 'Cd70', 'Ifng', 'Cd209', 'Ccl8', 'Tnf', 'Pdgfa', 'Wnt3', 'Il1b', 'Jag1', 'Ltb', 'Cxcl8', 'Il7', 'Lif', 'Col6a3', 'Cdh1', 'Itgb2', 'Itgb1', 'Efna1', 'Efnb1', 'Bmp7', 'Cdh5', 'Fgf2', 'Angpt2', 'Hla-dqa1', 'Il10', 'Ptprc', 'Tgfb3', 'Il6', 'Wnt9a', 'Ccl18', 'Cxcl9', 'Anxa1', 'Il12b', 'Vegfd', 'Cd86', 'Rarres2', 'Ins', 'Fgf1', 'Clcf1', 'Osm', 'Cxcl10', 'Nppc', 'Cxcl5', 'Clec2b', 'Sell', 'App', 'Il2', 'Fgf7', 'Inhbb', 'Clec2d', 'Tgfb1', 'Adgre5', 'Esam', 'Angpt1', 'Il16', 'Hla-dpa1', 'Cx3cl1', 'Col1a2', 'Hla-dpb1', 'Ccl15', 'Fgf18', 'Nrg1', 'Ccl11', 'Efna5', 'Bmp2', 'Cd80', 'Il24', 'Kitlg', 'Faslg', 'Gas6', 'Vegfb', 'Col4a5', 'Icam2', 'Hgf', 'Itga9', 'Bmp5', 'Igf1', 'Lgals9', 'Il36g', 'Hla-dra', 'Il34', 'Pdgfc', 'Vwf', 'Tnfsf4', 'Wnt5a', 'Tnfsf14', 'Pdgfd', 'Icoslg', 'Wnt10b', 'Col6a2', 'Icam1', 'Col6a1', 'Dll4', 'Cd69', 'Pdcd1lg2', 'Col4a2', 'Wnt11', 'Fn1', 'Cd40lg', 'Il11'], are not valid obs/ var names or indices."

I tried to convert my human gene symbols to the upcase+lowercase format but returned error:

Please suggest what is the best solution, thank you so much!