def umi_hist_facet_stratify(br: CellBranch,
facet: str,
stratify: str,
histtype="step",
xlim=(0, 12500),
**kwargs):
# TODO: use subplots outside of loop and return single ax
for indication, brr in br.groupby(facet):
print(indication)
fig, ax = plt.subplots(figsize=(20, 5))
for lane, brrr in brr.groupby(stratify):
brrr.rna.hist(bins=200,
ax=ax,
labels=brrr.meta[stratify],
histtype=histtype,
**kwargs)
ax.set_xlim(*xlim)
plt.show()
def test_process_aliasing(root_path_2, sample_paths, alias_spec):
cf = CellBranch.from_input_dirs(root_path_2, sample_paths, spec=alias_spec, mode="rna")
cf.process.process_1()
cf.process.process_2()
return cf
def test_process_chain(root_path, build_root_fix, process_chain_spec):
cf = CellBranch(root_dir=root_path, spec=process_chain_spec)
cf.process.normalize()
cf.process.test_process()
return cf
def test_norm_reduce(root_path, build_root_fix, norm_reduce_spec, test_norm_fix):
cf = CellBranch(root_dir=root_path, spec=norm_reduce_spec)
cf.process.reduce()
return cf
def test_norm_fix(root_path, build_root_fix, norm_spec):
cf = CellBranch(root_dir=root_path, spec=norm_spec)
cf.process.normalize()
return cf
def test_from_input_dirs_fix(root_path, sample_paths):
cf = CellBranch.from_input_dirs(root_path, sample_paths, mode="rna")
_ = cf.meta
_ = cf.rna
return sample_paths
def test_from_input_dirs_single(root_path, sample_1):
cf = CellBranch.from_input_dirs(root_path, sample_1, mode="rna")
_ = cf.meta
_ = cf.rna
return sample_1
def build_root_fix(root_path, metadata):
cf = CellBranch.from_metadata(root_path, metadata)
_ = cf.meta
_ = cf.rna
assert len(cf.meta.columns) > 0
return cf