cellphonedb results visualization
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Entering edit mode
18 months ago
piotto ▴ 20

I want to visualize cellphonedb results but I get several error. I do visualization by ktplotspy package. First, I read the required files based on its tutorials and when I try to create the heatmap, it gives an error:

code:

kpy.plot_cpdb_heatmap(
        adata=adata,
        pvals=pvals,
        celltype_key="celltype",
        figsize = (5,5),
        title = "Sum of significant interactions"
    )

Error:

>Traceback (most recent call last):
  File "/Users/pedram/opt/anaconda3/envs/CPDB-New/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3803, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'celltype'


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

>Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/pedram/opt/anaconda3/envs/CPDB-New/lib/python3.8/site-packages/ktplotspy/plot/plot_cpdb.py", line 181, in plot_cpdb
    metadata = ensure_categorical(meta=metadata, key=celltype_key)
  File "/Users/pedram/opt/anaconda3/envs/CPDB-New/lib/python3.8/site-packages/ktplotspy/utils/support.py", line 111, in ensure_categorical
    if not is_categorical(meta[key]):
  File "/Users/pedram/opt/anaconda3/envs/CPDB-New/lib/python3.8/site-packages/pandas/core/frame.py", line 3805, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/Users/pedram/opt/anaconda3/envs/CPDB-New/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3805, in get_loc
    raise KeyError(key) from err
KeyError: 'celltype'

I guess it might be related to the h5ad file but not sure. Also, if there is any suggestion regarding visualization of cpdb results, I welcome.

cellphonedb ktplotspy cpdb visulization • 1.2k views
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Entering edit mode

Did you solve this? I am struggling with the same issue...

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I had this same issue and I was able to resolve it by noting that my cell type annotation column in my adata frame object had a different name. Once I replaced "celltype" with the correct column, I was able to solve this issue

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