def buildVitessceConfig(adata, area_name):
vc = VitessceConfig("Developing human neocortex: gestational week 20")
dataset = vc.add_dataset(area_name).add_object(
# The`add_object()` function converts the AnnData data structure into a [Zarr]
# (https://zarr.readthedocs.io/en/stable/) store that is compatible with Vitessce.
AnnDataWrapper(adata,
mappings_obsm=["X_tsne"],
mappings_obsm_names=["t-SNE"],
expression_matrix="X",
spatial_centroid_obsm="X_spatial"))
spatial_plot = vc.add_view(dataset, cm.SPATIAL)
tsne_plot = vc.add_view(dataset, cm.SCATTERPLOT, mapping="t-SNE")
heatmap = vc.add_view(dataset, cm.HEATMAP)
genes_list = vc.add_view(dataset, cm.GENES)
vc.layout((spatial_plot | tsne_plot) / (heatmap | genes_list))
return vc
def test_config_set_layout_single_view(self):
vc = VitessceConfig()
my_dataset = vc.add_dataset(name='My Dataset')
my_view = vc.add_view(cm.SPATIAL, dataset=my_dataset)
vc.layout(my_view)
vc_dict = vc.to_dict()
vc_json = json.dumps(vc_dict)
self.assertEqual(
vc_dict, {
"version":
"1.0.4",
"name":
"",
"description":
"",
"datasets": [{
'uid': 'A',
'name': 'My Dataset',
'files': []
}],
'coordinationSpace': {
'dataset': {
'A': 'A'
},
},
"layout": [{
'component': 'spatial',
'coordinationScopes': {
'dataset': 'A',
},
'x': 0,
'y': 0,
'h': 12,
'w': 12,
}],
"initStrategy":
"auto"
})