Bug report [BUG] create_cistopic_object fails with InvalidIndexError whenever min cell != 1

[dmuratli]

Describe the bug

In create_cistopic_object (src/pycisTopic/cistopic_class.py), the min_cell filtering branch indexes the region_data DataFrame with numpy-style 2D syntax:

if min_cell != 1:
    selected_regions = region_data.cisTopic_nr_acc >= min_cell
    fragment_matrix = fragment_matrix[selected_regions, :]
    binary_matrix = binary_matrix[selected_regions, :]
    region_data = region_data[selected_regions, :]   # <-- fails
    region_names = region_data.index.to_list()

region_data is a pandas DataFrame returned by region_names_to_coordinates, so region_data[(boolean_Series, slice)] raises pandas.errors.InvalidIndexError. The call fails for any value of min_cell other than the default of 1, including min_cell=0, since the guard tests the parameter value rather than whether any region is actually dropped.

The equivalent min_frag branch a few lines above handles the same situation correctly with .loc:

if min_frag != 1:
    selected_cells = cell_data.cisTopic_nr_frag >= min_frag
    ...
    cell_data = cell_data.loc[selected_cells,]

This suggests the region block was written by analogy and the .loc was dropped.

The default min_cell=1 skips the branch entirely, which is likely why this has gone unnoticed.

To reproduce

import numpy as np
from scipy.sparse import csr_matrix
from pycisTopic.cistopic_class import create_cistopic_object

rng = np.random.default_rng(0)
n_regions, n_cells = 200, 50
fragment_matrix = csr_matrix(rng.poisson(0.3, size=(n_regions, n_cells)).astype(np.int32))

region_names = [f"chr1:{i * 1000}-{i * 1000 + 500}" for i in range(n_regions)]
cell_names = [f"cell_{i}" for i in range(n_cells)]

# Works
create_cistopic_object(fragment_matrix, cell_names, region_names)

# Raises InvalidIndexError
create_cistopic_object(fragment_matrix, cell_names, region_names, min_cell=10)

Expected behaviour

Regions detected in fewer than min_cell cells are dropped and a CistopicObject is returned.

Actual behaviour

Traceback (most recent call last):
  File ".../pycisTopic/cistopic_class.py", line 637, in create_cistopic_object
    region_data = region_data[selected_regions, :]
                  ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File ".../pandas/core/frame.py", line 3805, in __getitem__
    indexer = self.columns.get_loc(key)
  File ".../pandas/core/indexes/base.py", line 3807, in get_loc
    self._check_indexing_error(key)
  File ".../pandas/core/indexes/base.py", line 5963, in _check_indexing_error
    raise InvalidIndexError(key)
pandas.errors.InvalidIndexError: (RegionIDs
GL000009.2:124435-125319    True
...
chrX:155880858-155881766    True
Name: cisTopic_nr_acc, Length: 153377, dtype: bool, slice(None, None, None))

Versions

• pycisTopic: 2.0a0 (installed as a git dependency of SCENIC+)
• pandas: 1.5.0
• numpy: 1.26.4
• Python: 3.11.8

Suggested fix

region_data = region_data.loc[selected_regions]