def test_prepare_n_test_points(self, adata_cflare):
model = create_model(adata_cflare)
model = model.prepare(adata_cflare.var_names[0],
"0",
n_test_points=300)
assert len(model.x_test) == 300
def test_create_models_lineage_specific_fallback(self, adata: AnnData):
m1 = create_model(adata)
m2 = GAM(adata)
models = _create_models(
{"foo": {"baz": m1, "*": m2}, "bar": {"quux": m2, "*": m1}},
["foo", "bar"],
["baz", "quux", "quas", "wex"],
)
assert set(models.keys()) == {"foo", "bar"}
for k, vs in models.items():
assert set(vs.keys()) == {"baz", "quux", "quas", "wex"}
assert isinstance(models["foo"]["baz"], type(m1))
assert models["foo"]["baz"] is not m1
for l in {"quux", "quas", "wex"}:
assert isinstance(models["foo"][l], type(m2))
assert models["foo"][l] is not m2
assert isinstance(models["bar"]["quux"], type(m2))
assert models["bar"]["quux"] is not m2
for l in {"baz", "quas", "wex"}:
assert isinstance(models["bar"][l], type(m1))
assert models["bar"][l] is not m1
def test_from_model_normal_run(self, adata_cflare: AnnData):
m = create_model(adata_cflare).prepare(adata_cflare.var_names[0],
"1").fit()
m.predict()
m.confidence_interval()
fm = FittedModel.from_model(m)
assert fm.prepared
assert fm._gene == m._gene
assert fm._lineage == m._lineage
np.testing.assert_array_equal(fm.x_test, m.x_test)
assert fm.x_test is not m.x_test
np.testing.assert_array_equal(fm.y_test, m.y_test)
assert fm.y_test is not m.y_test
np.testing.assert_array_equal(fm.conf_int, m.conf_int)
assert fm.conf_int is not m.conf_int
np.testing.assert_array_equal(fm.x_all, m.x_all)
assert fm.x_all is not m.x_all
np.testing.assert_array_equal(fm.y_all, m.y_all)
assert fm.y_all is not m.y_all
np.testing.assert_array_equal(fm.w_all, m.w_all)
assert fm.y_all is not m.w_all
def test_invalid_n_perms(self, adata_cflare):
model = create_model(adata_cflare)
with pytest.raises(ValueError):
_ = cr.tl.gene_importance(adata_cflare,
model,
adata_cflare.var_names[:10],
"0",
n_perms=-1)
def test_create_models_1_model(self, adata: AnnData):
m = create_model(adata)
models = _create_models(m, ["foo"], ["bar"])
assert set(models.keys()) == {"foo"}
assert set(models["foo"].keys()) == {"bar"}
assert isinstance(models["foo"]["bar"], type(m))
assert models["foo"]["bar"] is not m
def sklearn_model(adata_cflare: AnnData) -> SKLearnModel:
m = create_model(adata_cflare)
assert isinstance(m, SKLearnModel), m
m.prepare(adata_cflare.var_names[0], "0").fit()
m.predict()
m.confidence_interval()
return m
def test_confidence_interval(self, adata_cflare):
model = create_model(adata_cflare)
model = model.prepare(adata_cflare.var_names[0], "0").fit()
_ = model.predict()
ci = model.confidence_interval()
assert isinstance(model.conf_int, np.ndarray)
assert len(model.y_test) == len(model.conf_int)
assert ci is model.conf_int
def test_perms_fdr_correction(self, adata_cflare):
model = create_model(adata_cflare)
res = cr.tl.gene_importance(adata_cflare,
model,
adata_cflare.var_names,
"0",
n_perms=10)
assert "pval" in res.columns
assert "qval" in res.columns
def test_predict(self, adata_cflare):
model = create_model(adata_cflare)
model = model.prepare(adata_cflare.var_names[0], "0").fit()
y_hat = model.predict()
assert isinstance(model.y_test, np.ndarray)
assert len(model.x_test) == len(model.y_test)
assert y_hat is model.y_test
assert model.conf_int is None
def test_heatmap_lineages(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.heatmap(
adata,
model,
GENES[:10],
kind="lineages",
time_key="latent_time",
dpi=DPI,
save=fpath,
)
def test_perms_no_fdr_correction(self, adata_cr: AnnData):
model = create_model(adata_cr)
res = cr.tl.gene_importance(adata_cr,
model,
adata_cr.var_names,
"0",
n_perms=10,
fdr_correction=None)
assert "pval" in res.columns
assert "qval" not in res.columns
def test_cluster_lineage(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.cluster_lineage(
adata,
model,
adata.var_names[:10],
"0",
time_key="latent_time",
dpi=DPI,
save=fpath,
)
def test_prepare_normal_run(self, adata_cflare):
model = create_model(adata_cflare)
model = model.prepare(adata_cflare.var_names[0], "0")
assert isinstance(model.x, np.ndarray)
assert isinstance(model.w, np.ndarray)
assert isinstance(model.y, np.ndarray)
assert isinstance(model.x_test, np.ndarray)
assert len(model.x_test) == 200
assert model.y_test is None
assert model.conf_int is None
def test_trends(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
adata.var_names[:3],
data_key="Ms",
dirname="trends_simple",
dpi=DPI,
save=fpath,
)
def test_trends_same_plot(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
adata.var_names[:3],
data_key="Ms",
same_plot=True,
dpi=DPI,
save=fpath,
)
def test_heatmap_genes(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.heatmap(
adata,
model,
adata.var_names[:10],
kind="genes",
time_key="latent_time",
dpi=DPI,
save=fpath,
)
def test_trends_lineage_cmap(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[0],
data_key="Ms",
same_plot=True,
lineage_cmap=cm.Set2,
dpi=DPI,
save=fpath,
)
def test_trends_lineage_cell_color(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[0],
data_key="Ms",
same_plot=True,
cell_color="red",
dpi=DPI,
save=fpath,
)
def test_trends_margins(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[0],
data_key="Ms",
same_plot=True,
margins=0.2,
dpi=DPI,
save=fpath,
)
def test_heatmap_cmap(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.heatmap(
adata,
model,
GENES[:5],
kind="genes",
time_key="latent_time",
cmap=cm.viridis,
dpi=DPI,
save=fpath,
)
def test_trends_lineage_alpha(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
adata.var_names[0],
data_key="Ms",
same_plot=True,
lineage_alpha=1,
dpi=DPI,
save=fpath,
)
def test_cluster_lineage_no_norm(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.cluster_lineage(
adata,
model,
GENES[:10],
"0",
time_key="latent_time",
norm=False,
dpi=DPI,
save=fpath,
)
def test_heatmap_lineage_height(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.heatmap(
adata,
model,
adata.var_names[:10],
kind="lineages",
time_key="latent_time",
lineage_height=0.2,
dpi=DPI,
save=fpath,
)
def test_trends_cbar(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[0],
data_key="Ms",
same_plot=True,
show_cbar=False,
dpi=DPI,
save=fpath,
)
def test_trends_cell_alpha(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[0],
data_key="Ms",
same_plot=True,
cell_alpha=0,
dpi=DPI,
save=fpath,
)
def test_trends_sharey(self, adata: AnnData, fpath: str):
model = create_model(adata)
cr.pl.gene_trends(
adata,
model,
GENES[:3],
data_key="Ms",
sharey=False,
dirname="trends_sharey",
dpi=DPI,
save=fpath,
)
def test_no_perms(self, adata_cflare):
model = create_model(adata_cflare)
res = cr.tl.gene_importance(adata_cflare,
model,
adata_cflare.var_names[:10],
"0",
n_perms=None)
assert isinstance(res, pd.DataFrame)
assert res.shape == (10, 1)
assert set(res.index) == set(adata_cflare.var_names[:10])
assert "importance" in res.columns
def test_create_models_lineage_specific(self, adata: AnnData):
m1 = create_model(adata)
m2 = GAM(adata)
models = _create_models(
{"foo": {"bar": m1, "baz": m2}}, ["foo"], ["bar", "baz"]
)
assert set(models["foo"].keys()) == {"bar", "baz"}
assert isinstance(models["foo"]["bar"], type(m1))
assert models["foo"]["bar"] is not m1
assert isinstance(models["foo"]["baz"], type(m2))
assert models["foo"]["baz"] is not m2
def test_heatmap_start_end_clusters(self, adata: AnnData, fpath: Path):
model = create_model(adata)
cr.pl.heatmap(
adata,
model,
adata.var_names[:10],
kind="lineages",
time_key="latent_time",
start_lineage="0",
end_lineage="1",
dpi=DPI,
save=fpath,
)
def test_model_1_lineage(self, adata_cflare):
adata_cflare.obsm[AbsProbKey.FORWARD.s] = Lineage(np.ones(
(adata_cflare.n_obs, 1)),
names=["foo"])
model = create_model(adata_cflare)
model = model.prepare(adata_cflare.var_names[0],
"foo",
n_test_points=100).fit()
_ = model.predict()
assert model.x_test.shape == (100, 1)
xtest, xall = model.x_test, model.x_all
np.testing.assert_allclose(np.r_[xtest[0], xtest[-1]],
np.r_[np.min(xall),
np.max(xall)])