def test_plot_kwargs(self, ligrec_result: Mapping[str, pd.DataFrame]):
# color_on is intentionally ignored
pl.ligrec(ligrec_result,
grid=False,
color_on="square",
x_padding=2,
y_padding=2)
def test_invalid_means_range_size(self,
ligrec_result: Mapping[str,
pd.DataFrame]):
with pytest.raises(
ValueError,
match=
r"Expected `means_range` to be a sequence of size `2`, found `3`."
):
pl.ligrec(ligrec_result, means_range=[0, 1, 2])
def test_all_interactions_empty(self,
ligrec_result: Mapping[str, pd.DataFrame]):
empty = pd.DataFrame(np.nan,
index=ligrec_result["pvalues"].index,
columns=ligrec_result["pvalues"].columns)
with pytest.raises(
ValueError,
match=
r"After removing rows with only NaN interactions, none remain."
):
pl.ligrec({
"means": empty,
"pvalues": empty,
"metadata": empty
},
remove_empty_interactions=True)
def test_plot_swap_axes(self, ligrec_result: Mapping[str, pd.DataFrame]):
pl.ligrec(ligrec_result, swap_axes=True)
def test_plot_dendrogram_both(self, ligrec_result: Mapping[str,
pd.DataFrame]):
np.random.seed(42)
pl.ligrec(ligrec_result, dendrogram="both")
def test_plot_dendrogram_clusters(self,
ligrec_result: Mapping[str,
pd.DataFrame]):
# this currently "fails" (i.e. no dendrogram)
np.random.seed(42)
pl.ligrec(ligrec_result, dendrogram="interacting_clusters")
def test_plot_dendrogram_pairs(self, ligrec_result: Mapping[str,
pd.DataFrame]):
np.random.seed(42)
pl.ligrec(ligrec_result, dendrogram="interacting_molecules")
def test_plot_means_range(self, ligrec_result: Mapping[str, pd.DataFrame]):
pl.ligrec(ligrec_result, means_range=(0.5, 1))
def test_invalid_key(self, adata: AnnData):
with pytest.raises(
KeyError,
match=r"Key `foobar_ligrec` not found in `adata.uns`."):
pl.ligrec(adata, cluster_key="foobar")
def test_plot_cmap(self, ligrec_result: Mapping[str, pd.DataFrame]):
pl.ligrec(ligrec_result, cmap="inferno")
def test_plot_target_clusters(self, ligrec_result: Mapping[str,
pd.DataFrame]):
tgt_cls = ligrec_result["pvalues"].columns.get_level_values(1)[0]
pl.ligrec(ligrec_result, target_groups=tgt_cls)
def test_plot_source_clusters(self, ligrec_result: Mapping[str,
pd.DataFrame]):
src_cls = ligrec_result["pvalues"].columns.get_level_values(0)[0]
pl.ligrec(ligrec_result, source_groups=src_cls)
def test_invalid_clusters(self, ligrec_result: Mapping[str, pd.DataFrame]):
with pytest.raises(ValueError,
match=r"No valid clusters have been selected."):
pl.ligrec(ligrec_result, source_groups="foo", target_groups="bar")
def test_invalid_alpha(self, ligrec_result: Mapping[str, pd.DataFrame]):
with pytest.raises(ValueError, match=r"Expected `alpha`"):
pl.ligrec(ligrec_result, alpha=1.2)
def test_valid_key_invalid_object(self, adata: AnnData):
adata.uns["foobar_ligrec"] = "baz"
with pytest.raises(TypeError,
match=r"Expected `adata` .+ found `str`."):
pl.ligrec(adata, cluster_key="foobar")
def test_plot_swap_axes_dedrogram(self,
ligrec_result: Mapping[str,
pd.DataFrame]):
pl.ligrec(ligrec_result,
swap_axes=True,
dendrogram="interacting_molecules")
def test_plot_alpha(self, ligrec_result: Mapping[str, pd.DataFrame]):
pl.ligrec(ligrec_result, alpha=1)
def test_plot_no_remove_empty_interactions(
self, ligrec_result: Mapping[str, pd.DataFrame]):
tmp = deepcopy(ligrec_result)
tmp["pvalues"].values[:2, :] = np.nan
pl.ligrec(tmp, remove_empty_interactions=False)
def test_plot_pvalue_threshold(self, ligrec_result: Mapping[str,
pd.DataFrame]):
pl.ligrec(ligrec_result, pvalue_threshold=0.05)
def test_invalid_type(self):
with pytest.raises(TypeError,
match=r"Expected `adata` .+ found `int`."):
pl.ligrec(42)
