pySCENIC PBMC10k_SCENIC-protocol-CLI 版本冲突导致的报错记录

scanpy 1.4.1和1.4.3报错： 1.5.1和1.8.1问题消失 (低版本不行)

f_mtx_dir = '/Users/yangl/Documents/work/python/filtered_feature_bc_matrix'
adata = sc.read_10x_mtx(
f_mtx_dir , # the directory with the `.mtx` file
var_names='gene_symbols', # use gene symbols for the variable names (variables-axis index)
cache=False)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/var/folders/1_/cs50ltcn0zl1h2b3xgkt8pd00000gn/T/ipykernel_25497/3803800128.py in <module>
      1 f_mtx_dir = '/Users/yangl/Documents/work/python/filtered_feature_bc_matrix'
      2 
----> 3 adata = sc.read_10x_mtx(
      4     f_mtx_dir ,                 # the directory with the `.mtx` file
      5     var_names='gene_symbols',   # use gene symbols for the variable names (variables-axis index)

~/Library/Python/3.8/lib/python/site-packages/scanpy/readwrite.py in read_10x_mtx(path, var_names, make_unique, cache, gex_only)
    241     genefile_exists = (path / 'genes.tsv').is_file()
    242     read = _read_legacy_10x_mtx if genefile_exists else _read_v3_10x_mtx
--> 243     adata = read(
    244         str(path),
    245         var_names=var_names,

~/Library/Python/3.8/lib/python/site-packages/scanpy/readwrite.py in _read_v3_10x_mtx(path, var_names, make_unique, cache)
    287         if make_unique:
    288             var_names = anndata.utils.make_index_unique(pd.Index(var_names))
--> 289         adata.var_names = var_names
    290         adata.var['gene_ids'] = genes[0].values
    291     elif var_names == 'gene_ids':

~/Library/Python/3.8/lib/python/site-packages/anndata/_core/anndata.py in var_names(self, names)
    889     @var_names.setter
    890     def var_names(self, names: Sequence[str]):
--> 891         names = self._prep_dim_index(names, "var")
    892         self._set_dim_index(names, "var")
    893 

~/Library/Python/3.8/lib/python/site-packages/anndata/_core/anndata.py in _prep_dim_index(self, value, attr)
    810             value.name, (str, type(None))
    811         ):
--> 812             raise ValueError(
    813                 f"AnnData expects .{attr}.index.name to be a string or None, "
    814                 f"but you passed a name of type {type(value.name).__name__!r}"

ValueError: AnnData expects .var.index.name to be a string or None, but you passed a name of type 'int64'

numpy 1.20.3报错：低版本numpy==1.15.0以下不行，1.15.1好像可以（见链接） 1.17.3 1.17.5不行，这个不重要，保证其正常会导致其他包冲突，遂放弃

nGenesDetectedPerCell = np.sum(adata.X>0, axis=1)
percentiles = nGenesDetectedPerCell.quantile([.01, .05, .10, .50, 1])
print(percentiles)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/var/folders/1_/cs50ltcn0zl1h2b3xgkt8pd00000gn/T/ipykernel_42667/3438945105.py in <module>
      1 nGenesDetectedPerCell = np.sum(adata.X>0, axis=1)
----> 2 percentiles = nGenesDetectedPerCell.quantile([.01, .05, .10, .50, 1])
      3 print(percentiles)

AttributeError: 'matrix' object has no attribute 'quantile'

from scanpy.plotting._tools.scatterplots import plot_scatter命令报错

importerror: cannot import name 'plot_scatter' from 'scanpy.plotting._tools.scatterplots'

解决办法： pip install scanpy==1.4.2   （高版本1.4.5.1后scanpy.plotting._tools.scatterplots中没有plot_scatter函数）

报错：AttributeError: module 'igraph' has no attribute 'Graph'，解决办法（来源）：

pip install python-igraph #如果安装了igraph or jgraph (pip install igraph / pip install jgraph) ，先卸载

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