ktplotspy绘制CellphoneDB结果弦图时tmpdf.index = complex_id处出现ValueError: Length mismatch

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报错内容

完整报错示例 
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---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[48], line 1
----> 1 kpy.plot_cpdb_chord(
      2     adata=adata_cpdb,
      3     cell_type1=".",
      4     cell_type2='.',
      5     means=means,
      6     pvals=pvals,
      7     deconvoluted=decon,
      8     celltype_key="celltype",
      9     link_offset=1,
     11     )

File ~/anaconda3/envs/jupyterlab/lib/python3.10/site-packages/ktplotspy/plot/plot_cpdb_chord.py:170, in plot_cpdb_chord(adata, means, pvals, deconvoluted, celltype_key, interaction, cell_type1, cell_type2, keep_celltypes, remove_self, layer, sector_colors, sector_text_kwargs, sector_radius_limit, equal_sector_size, same_producer_colors, link_colors, link_offset, link_kwargs, legend_width, legend_kwargs, **plot_cpdb_kwargs)
    168     simple_2[i] = re.sub(partner_2[i] + "_|_" + partner_2[i], "", simple_2[i])
    169 tmpdf = pd.concat([pd.DataFrame(zip(simple_1, partner_1)), pd.DataFrame(zip(partner_2, simple_2))])
--> 170 tmpdf.index = complex_id
    171 tmpdf.columns = ["id_a", "id_b"]
    172 _interactions_subset = pd.concat([_interactions_subset, tmpdf], axis=1)

File ~/anaconda3/envs/jupyterlab/lib/python3.10/site-packages/pandas/core/generic.py:6313, in NDFrame.__setattr__(self, name, value)
   6311 try:
   6312     object.__getattribute__(self, name)
-> 6313     return object.__setattr__(self, name, value)
   6314 except AttributeError:
   6315     pass

File properties.pyx:69, in pandas._libs.properties.AxisProperty.__set__()

File ~/anaconda3/envs/jupyterlab/lib/python3.10/site-packages/pandas/core/generic.py:814, in NDFrame._set_axis(self, axis, labels)
    809 """
    810 This is called from the cython code when we set the `index` attribute
    811 directly, e.g. `series.index = [1, 2, 3]`.
    812 """
    813 labels = ensure_index(labels)
--> 814 self._mgr.set_axis(axis, labels)
    815 self._clear_item_cache()

File ~/anaconda3/envs/jupyterlab/lib/python3.10/site-packages/pandas/core/internals/managers.py:238, in BaseBlockManager.set_axis(self, axis, new_labels)
    236 def set_axis(self, axis: AxisInt, new_labels: Index) -> None:
    237     # Caller is responsible for ensuring we have an Index object.
--> 238     self._validate_set_axis(axis, new_labels)
    239     self.axes[axis] = new_labels

File ~/anaconda3/envs/jupyterlab/lib/python3.10/site-packages/pandas/core/internals/base.py:98, in DataManager._validate_set_axis(self, axis, new_labels)
     95     pass
     97 elif new_len != old_len:
---> 98     raise ValueError(
     99         f"Length mismatch: Expected axis has {old_len} elements, new "
    100         f"values have {new_len} elements"
    101     )

ValueError: Length mismatch: Expected axis has 86 elements, new values have 78 elements

问题分析

是complex_id的长度小于tmpdf.index的长度。

源码根据interacting_pair字段将相互作用划分到complex_id或simple_id中，标准是这个字段里下划线的数量。

然后问题出在分隔出来的地方 

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_interactions_subset = interactions_subset.loc[complex_id].copy()
_interactions_subset_simp = interactions_subset.loc[simple_id].copy()


# 问题
complex_idx1 = [i for i, j in _interactions_subset.partner_b.items() if re.search("complex:", j)]
complex_idx2 = [i for i, j in _interactions_subset.partner_a.items() if re.search("complex:", j)]
# 问题


# complex_idx
simple_1 = list(_interactions_subset.loc[complex_idx1, "interacting_pair"])
simple_2 = list(_interactions_subset.loc[complex_idx2, "interacting_pair"])
partner_1 = [re.sub("complex:", "", b) for b in _interactions_subset.loc[complex_idx1, "partner_b"]]
partner_2 = [re.sub("complex:", "", a) for a in _interactions_subset.loc[complex_idx2, "partner_a"]]
for i, _ in enumerate(simple_1):
    simple_1[i] = re.sub(partner_1[i] + "_|_" + partner_1[i], "", simple_1[i])
for i, _ in enumerate(simple_2):
    simple_2[i] = re.sub(partner_2[i] + "_|_" + partner_2[i], "", simple_2[i])
tmpdf = pd.concat([pd.DataFrame(zip(simple_1, partner_1)), pd.DataFrame(zip(partner_2, simple_2))])
tmpdf.index = complex_id

在这个CellphoneDB结果里，partner_a和partner_b有同时包含complex:的情况，此时会有相同的行被划分到complex_idx1和complex_idx2中，从而导致tmpdf中有重复的部分，行数大于complex_id的长度。

解决方案

在作者修好之前，可以暂时先在取complex_idx2的时候，不选complex_idx1中存在的行。 

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complex_idx2 = [
    i for i, j in _interactions_subset.partner_a.items()
    if re.search("complex:", j) and i not in complex_idx1
]

03-19跟进

我已经提交PR修复了包括此BUG在内的2个问题w