[BUG] freyja plot failed

[Charles-Lou]

when i run freyja 2.0.3, some errors
freyja plot /home/lcxu/aggregate.tsv --output /home/lcxu/freyja.png --mincov 50 --lineages
Traceback (most recent call last):
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/indexing.py", line 2144, in _setitem_single_column
self.obj._mgr.column_setitem(
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1526, in column_setitem
col_mgr.setitem_inplace(idx, value)
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 2234, in setitem_inplace
arr[indexer] = value
~~~^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/arrays/arrow/array.py", line 2237, in setitem
value = self._maybe_convert_setitem_value(value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/arrays/string_arrow.py", line 298, in _maybe_convert_setitem_value
if len(value) and not (
^^^^^^^^^^
TypeError: len() of unsized object

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

Traceback (most recent call last):
File "/home/lcxu/miniconda3/envs/freyja/bin/freyja", line 10, in
sys.exit(cli())
^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/click/core.py", line 1569, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/click/core.py", line 1490, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/click/core.py", line 1970, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/click/core.py", line 1353, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/click/core.py", line 907, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/freyja/_cli.py", line 694, in plot
makePlot_simple(agg_df, lineages, output, config, lineage_info,
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/freyja/utils.py", line 391, in makePlot_simple
agg_df = prepLineageDict(agg_df, config=config,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/freyja/utils.py", line 262, in prepLineageDict
agg_d0.loc[:, 'lineages'] = agg_d0['lineages'].apply(lambda x:
~~~~~~~~~~^^^^^^^^^^^^^^^
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/indexing.py", line 938, in setitem
iloc._setitem_with_indexer(indexer, value, self.name)
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/indexing.py", line 1953, in _setitem_with_indexer
self._setitem_with_indexer_split_path(indexer, value, name)
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/indexing.py", line 1997, in _setitem_with_indexer_split_path
self._setitem_single_column(ilocs[0], value, pi)
File "/home/lcxu/miniconda3/envs/freyja/lib/python3.12/site-packages/pandas/core/indexing.py", line 2163, in _setitem_single_column
raise TypeError(
TypeError: Invalid value '[list(['SV.2', 'SV.1', 'PQ.16.1', 'SZ.3', 'PQ.17', 'PQ.1.2', 'PQ.36', 'PQ.17.2'])]' for dtype 'str'

aggregate.tsv

[gp201]

@Charles-Lou downgrading pandas to v2.x should fix that error.

[gp201]

More info:

In the pandas v3.0 the default dtype changes from object to str (https://pandas.pydata.org/docs/user_guide/migration-3-strings.html#string-migration-guide). Hence when a list is assigned to the column's str dtype it will fail.

To fix this we can do either of the following:

1. replace the values in the column

- agg_d0.loc[:, 'lineages'] = agg_d0['lineages'].apply(lambda x: 
+ agg_d0['lineages'] = agg_d0['lineages'].apply(lambda x: 

2. change the type

+ agg_d0['lineages'] = agg_d0['lineages'].astype(object)

Freyja/freyja/utils.py

Lines 301 to 303 in fbe00d2

	agg_d0.loc[:, 'lineages'] = agg_d0['lineages'].apply(lambda x:
	re.sub(' +', ' ', x)
	.split(' ')).copy()

Please feel free to correct me if I'm wrong

[Charles-Lou]

downgrading pandas to v2.x
@gp201 the method is effective