I am using version v4.1.1. When I include region_ref with a list of snps I get the following error (the plot is outputted correctly when removing this flag): Traceback (most recent call last):
File ".venv/lib/python3.12/site-packages/IPython/core/interactiveshell.py", line 3701, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
gwas.plot_mqq(
File ".venv/lib/python3.12/site-packages/gwaslab/info/g_object_helper.py", line 16, in _wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/g_Sumstats.py", line 1258, in plot_mqq
plot, log = _mqqplot(self, **params)
^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/io/io_process_kwargs.py", line 140, in wrapper
return func(**bound.arguments)
^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_aux_save_figure.py", line 165, in wrapper
raise e
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_aux_save_figure.py", line 161, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_plot_mqqplot.py", line 1117, in _mqqplot
sumstats = process_vcf(sumstats=sumstats,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_plot_regional2.py", line 1524, in process_vcf
lead_snp_genotype = GenotypeArray([ref_genotype["calldata/GT"][lead_snp_ref_index]]).to_n_alt()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/allel/model/ndarray.py", line 1553, in init
check_ndim(self.values, 3)
File ".venv/lib/python3.12/site-packages/allel/util.py", line 66, in check_ndim
raise TypeError('bad number of dimensions: expected %s; found %s' % (ndim, a.ndim))
TypeError: bad number of dimensions: expected 3; found 5
I am using version v4.1.1. When I include region_ref with a list of snps I get the following error (the plot is outputted correctly when removing this flag): Traceback (most recent call last):
File ".venv/lib/python3.12/site-packages/IPython/core/interactiveshell.py", line 3701, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
gwas.plot_mqq(
File ".venv/lib/python3.12/site-packages/gwaslab/info/g_object_helper.py", line 16, in _wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/g_Sumstats.py", line 1258, in plot_mqq
plot, log = _mqqplot(self, **params)
^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/io/io_process_kwargs.py", line 140, in wrapper
return func(**bound.arguments)
^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_aux_save_figure.py", line 165, in wrapper
raise e
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_aux_save_figure.py", line 161, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_plot_mqqplot.py", line 1117, in _mqqplot
sumstats = process_vcf(sumstats=sumstats,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/gwaslab/viz/viz_plot_regional2.py", line 1524, in process_vcf
lead_snp_genotype = GenotypeArray([ref_genotype["calldata/GT"][lead_snp_ref_index]]).to_n_alt()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".venv/lib/python3.12/site-packages/allel/model/ndarray.py", line 1553, in init
check_ndim(self.values, 3)
File ".venv/lib/python3.12/site-packages/allel/util.py", line 66, in check_ndim
raise TypeError('bad number of dimensions: expected %s; found %s' % (ndim, a.ndim))
TypeError: bad number of dimensions: expected 3; found 5