def check_colornorm(vmin=None, vmax=None, vcenter=None, norm=None):
from matplotlib.colors import Normalize
try:
from matplotlib.colors import TwoSlopeNorm as DivNorm
except ImportError:
# matplotlib<3.2
from matplotlib.colors import DivergingNorm as DivNorm
if norm is not None:
if (vmin is not None) or (vmax is not None) or (vcenter is not None):
raise ValueError(
'Passing both norm and vmin/vmax/vcenter is not allowed.')
else:
if vcenter is not None:
norm = DivNorm(vmin=vmin, vmax=vmax, vcenter=vcenter)
else:
norm = Normalize(vmin=vmin, vmax=vmax)
return norm
def test_scatter_embedding_add_outline_vmin_vmax_norm(image_comparer, check_same_image):
save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
pbmc = sc.datasets.pbmc68k_reduced()
sc.pl.embedding(
pbmc,
'X_umap',
color=['percent_mito', 'n_counts', 'bulk_labels', 'percent_mito'],
s=200,
frameon=False,
add_outline=True,
vmax=['p99.0', partial(np.percentile, q=90), None, 0.03],
vmin=0.01,
vcenter=[0.015, None, None, 0.025],
outline_color=('#555555', '0.9'),
outline_width=(0.5, 0.5),
cmap='viridis_r',
alpha=0.9,
wspace=0.5,
)
save_and_compare_images('master_embedding_outline_vmin_vmax')
import matplotlib as mpl, matplotlib.pyplot as plt
norm = mpl.colors.LogNorm()
with pytest.raises(
ValueError, match="Passing both norm and vmin/vmax/vcenter is not allowed."
):
sc.pl.embedding(
pbmc,
'X_umap',
color=['percent_mito', 'n_counts'],
norm=norm,
vmin=0,
vmax=1,
vcenter=0.5,
cmap='RdBu_r',
)
try:
from matplotlib.colors import TwoSlopeNorm as DivNorm
except ImportError:
# matplotlib<3.2
from matplotlib.colors import DivergingNorm as DivNorm
from matplotlib.colors import Normalize
norm = Normalize(0, 10000)
divnorm = DivNorm(200, 150, 6000)
# allowed
sc.pl.umap(
pbmc,
color=['n_counts', 'bulk_labels', 'percent_mito'],
frameon=False,
vmax=['p99.0', None, None],
vcenter=[0.015, None, None],
norm=[None, norm, norm],
wspace=0.5,
)
sc.pl.umap(
pbmc,
color=['n_counts', 'bulk_labels'],
frameon=False,
norm=norm,
wspace=0.5,
)
plt.savefig(FIGS / 'umap_norm_fig0.png')
plt.close()
sc.pl.umap(
pbmc,
color=['n_counts', 'bulk_labels'],
frameon=False,
norm=divnorm,
wspace=0.5,
)
plt.savefig(FIGS / 'umap_norm_fig1.png')
plt.close()
sc.pl.umap(
pbmc,
color=['n_counts', 'bulk_labels'],
frameon=False,
vcenter=200,
vmin=150,
vmax=6000,
wspace=0.5,
)
plt.savefig(FIGS / 'umap_norm_fig2.png')
plt.close()
check_same_image(FIGS / 'umap_norm_fig1.png', FIGS / 'umap_norm_fig2.png', tol=1)
with pytest.raises(AssertionError):
check_same_image(
FIGS / 'umap_norm_fig1.png', FIGS / 'umap_norm_fig0.png', tol=1
)