def test_plot_obs_categorical(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata)
cnt = viewer._controller
cnt.add_points(adata.obs["leiden"], key="leiden", layer_name="quas")
viewer.screenshot(dpi=DPI)
def test_plot_cont_cmap(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata, cmap="inferno")
cnt = viewer._controller
cnt.add_points(adata.obs_vector(adata.var_names[42]), layer_name="wex")
viewer.screenshot(dpi=DPI)
def test_plot_symbol(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata, symbol="square")
cnt = viewer._controller
cnt.add_points(adata.obs_vector(adata.var_names[42]), layer_name="foo")
viewer.screenshot(dpi=DPI)
def test_plot_obs_continuous(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata)
cnt = viewer._controller
cnt.add_points(np.random.RandomState(42).normal(size=adata.n_obs),
layer_name="quux")
viewer.screenshot(dpi=DPI)
def test_plot_cat_cmap(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata, palette="Set3")
cnt = viewer._controller
cnt.add_points(adata.obs["leiden"].astype("category"),
key="in_tissue",
layer_name="exort")
viewer.screenshot(dpi=DPI)
def test_add_not_categorical_series(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata)
cnt = viewer._controller
with pytest.raises(TypeError,
match=r"Expected a `categorical` type,.*"):
cnt.add_points(adata.obs["in_tissue"].astype(int),
layer_name="layer1")
def test_plot_blending(self, qtbot, adata: AnnData, napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata, blending="additive")
cnt = viewer._controller
for gene in adata.var_names[42:46]:
data = adata.obs_vector(gene)
if issparse(data): # ALayer handles sparsity, here we have to do it ourselves
data = data.X
cnt.add_points(data, layer_name=gene)
viewer.screenshot(dpi=DPI)
def test_plot_add_image(self, qtbot, adata: AnnData, napari_cont: ImageContainer):
from napari.layers import Image
viewer = napari_cont.interactive(adata)
cnt = viewer._controller
img = np.zeros((*napari_cont.shape, 3), dtype=np.float32)
img[..., 0] = 1.0 # all red image
napari_cont.add_img(img, layer="foobar")
cnt.add_image("foobar")
assert viewer._controller.view.layernames == {"V1_Adult_Mouse_Brain", "foobar"}
assert isinstance(viewer._controller.view.layers["foobar"], Image)
viewer.screenshot(dpi=DPI)
def test_add_same_layer(self, qtbot, adata: AnnData, napari_cont: ImageContainer, capsys):
from napari.layers import Points
s.logfile = sys.stderr
s.verbosity = 4
viewer = napari_cont.interactive(adata)
cnt = viewer._controller
data = np.random.normal(size=adata.n_obs)
cnt.add_points(data, layer_name="layer1")
cnt.add_points(np.random.normal(size=adata.n_obs), layer_name="layer1")
err = capsys.readouterr().err
assert "Layer `layer1` is already loaded" in err
assert len(viewer._controller.view.layers) == 2
assert viewer._controller.view.layernames == {"V1_Adult_Mouse_Brain", "layer1"}
assert isinstance(viewer._controller.view.layers["layer1"], Points)
np.testing.assert_array_equal(viewer._controller.view.layers["layer1"].metadata["data"], data)
def test_plot_simple_canvas(self, qtbot, adata: AnnData,
napari_cont: ImageContainer):
viewer = napari_cont.interactive(adata)
viewer.screenshot(dpi=DPI)
