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jianhuupenn / TESLA

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
MIT License
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An error had occurred #6

Open rwkw23 opened 10 months ago

rwkw23 commented 10 months ago

enhanced_exp_adata.obs[g]=enhanced_exp_adata.X[:,enhanced_exp_adata.var.index==g] Traceback (most recent call last): File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2895, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'CD151'

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

Traceback (most recent call last): File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/generic.py", line 3574, in _set_item loc = self._info_axis.get_loc(key) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc raise KeyError(key) from err KeyError: 'CD151'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/frame.py", line 3040, in setitem self._set_item(key, value) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/frame.py", line 3117, in _set_item NDFrame._set_item(self, key, value) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/generic.py", line 3577, in _set_item self._mgr.insert(len(self._info_axis), key, value) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/internals/managers.py", line 1189, in ins ert block = makeblock(values=value, ndim=self.ndim, placement=slice(loc, loc + 1)) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/internals/blocks.py", line 2722, in make block return klass(values, ndim=ndim, placement=placement) File "/home/ZRZ/miniconda3/envs/TESLA/lib/python3.7/site-packages/pandas/core/internals/blocks.py", line 131, in init f"Wrong number of items passed {len(self.values)}, " ValueError: Wrong number of items passed 0, placement implies 1

how can I solve this problem？

jianhuupenn commented 10 months ago

Thanks for your interest in our method. It seems the gene "CD151" is not presented or filtered out in your original expression matrix. I would suggest to check the expression of CD151 in your raw data.

rwkw23 commented 10 months ago

Thanks for your interest in our method. It seems the gene "CD151" is not presented or filtered out in your original expression matrix. I would suggest to check the expression of CD151 in your raw data.

Hello, I encountered the following error while running the tutorial you provided. Do you have any good solutions to this issue?

Haz1y commented 4 months ago

How can multiple structures like this be accurately segmented into individual contours rather than one, as it results in many empty spots in the filled area, such as the black region in the image below, where there is no organization detected and thus no RNA present?

image image