KeyError

[Inbarpl]

Hi again,
Sorry but I'm not good with python
Trying to generate visualization according to T3 with my input data
but I keep getting this Error
I'v tried altering celltype_key value but could no understand what is the problem here
Thank you very much in advance
Inbar:

kpy.plot_cpdb(
adata = adata,
cell_type1 = "0|15|11",
cell_type2 = "2",
means = cpdb_results['means'],
pvals = cpdb_results['relevant_interactions'],
celltype_key = "cell_labels",
genes = ["TGFB2", "CSF1R", "COL1A2"],
figsize = (11,4),
title = "Interactions_V1_V2",
max_size = 5,
highlight_size = 0.75,
degs_analysis = True,
standard_scale = True,
interaction_scores = cpdb_results['interaction_scores'],
scale_alpha_by_interaction_scores=True,
)

KeyError Traceback (most recent call last)
File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/pandas/core/indexes/base.py:3653, in Index.get_loc(self, key)
3652 try:
-> 3653 return self._engine.get_loc(casted_key)
3654 except KeyError as err:

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/pandas/_libs/index.pyx:147, in pandas._libs.index.IndexEngine.get_loc()

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/pandas/_libs/index.pyx:176, in pandas._libs.index.IndexEngine.get_loc()

File pandas/_libs/hashtable_class_helper.pxi:7080, in pandas._libs.hashtable.PyObjectHashTable.get_item()

File pandas/_libs/hashtable_class_helper.pxi:7088, in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'cell_labels'

The above exception was the direct cause of the following exception:

KeyError Traceback (most recent call last)
Cell In[30], line 1
----> 1 kpy.plot_cpdb(
2 adata = adata,
3 cell_type1 = "0|15|11",
4 cell_type2 = "2",
5 means = cpdb_results['means'],
6 pvals = cpdb_results['relevant_interactions'],
7 celltype_key = "cell_labels",
8 genes = ["TGFB2", "CSF1R", "COL1A2"],
9 figsize = (11,4),
10 title = "Interactions_V1_V2",
11 max_size = 5,
12 highlight_size = 0.75,
13 degs_analysis = True,
14 standard_scale = True,
15 interaction_scores = cpdb_results['interaction_scores'],
16 scale_alpha_by_interaction_scores=True,
17 )

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/ktplotspy/plot/plot_cpdb.py:230, in plot_cpdb(adata, cell_type1, cell_type2, means, pvals, celltype_key, interaction_scores, cellsign, degs_analysis, splitby_key, alpha, keep_significant_only, genes, gene_family, custom_gene_family, standard_scale, cluster_rows, cmap_name, max_size, max_highlight_size, default_style, highlight_col, highlight_size, special_character_regex_pattern, exclude_interactions, title, return_table, figsize, min_interaction_score, scale_alpha_by_interaction_scores, scale_alpha_by_cellsign, filter_by_cellsign, keep_id_cp_interaction)
228 else:
229 query = [i for i in means_mat.interacting_pair if re.search("|".join(genes), i)]
--> 230 metadata = ensure_categorical(meta=metadata, key=celltype_key)
231 # prepare regex query for celltypes
232 if splitby_key is not None:

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/ktplotspy/utils/support.py:111, in ensure_categorical(meta, key)
96 def ensure_categorical(meta: pd.DataFrame, key: str) -> pd.DataFrame:
97 """Enforce categorical columns.
98
99 Parameters
(...)
109 Table with formatted column.
110 """
--> 111 if not is_categorical(meta[key]):
112 meta[key] = meta[key].astype("category")
113 return meta

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/pandas/core/frame.py:3761, in DataFrame.getitem(self, key)
3759 if self.columns.nlevels > 1:
3760 return self._getitem_multilevel(key)
-> 3761 indexer = self.columns.get_loc(key)
3762 if is_integer(indexer):
3763 indexer = [indexer]

File ~/A/projects_new/Michal_S_cellphoneDB/miniconda3/envs/cpdbv5/lib/python3.8/site-packages/pandas/core/indexes/base.py:3655, in Index.get_loc(self, key)
3653 return self._engine.get_loc(casted_key)
3654 except KeyError as err:
-> 3655 raise KeyError(key) from err
3656 except TypeError:
3657 # If we have a listlike key, _check_indexing_error will raise
3658 # InvalidIndexError. Otherwise we fall through and re-raise
3659 # the TypeError.
3660 self._check_indexing_error(key)

KeyError: 'cell_labels'

[datasome]

Hi Inbarpl,

ktplotspy is an external package to CellphoneDB - if what I'm about to write below doesn't help, you may want to raise an issue on https://github.com/zktuong/ktplotspy instead.

However, from what I see in line 230 of https://github.com/zktuong/ktplotspy/blob/master/ktplotspy/plot/plot_cpdb.py, it looks as if you may not have the column 'cell_labels' in your adata.obs - do you?
See also https://ktplotspy.readthedocs.io/en/latest/notebooks/tutorial.html on the use of plot_cpdb function - if that helps.

Best,

Robert.