Could not get 'spatial' show up in the browser

[d5423197]

Hello there,

below is my code:

from vitessce import VitessceConfig, AnnDataWrapper, Component as cm
from urllib.parse import quote_plus
import json

zarr_path = r"D:\data\h5\adata_processed.zarr"

vc = VitessceConfig(schema_version="1.0.15", name='Habib et al', description='COVID-19 Healthy Donor Brain')
dataset = vc.add_dataset(name='Brain').add_object(
    AnnDataWrapper(
        adata_path=zarr_path,
        obs_embedding_paths=["obsm/X_umap"],
        obs_embedding_names=["UMAP"],
        obs_set_paths=["obs/leiden"],
        obs_set_names=["Leiden"],
        obs_feature_matrix_path="X",
        feature_filter_path="var/highly_variable",
        obs_locations_path="obsm/spatial"
    ))

# 创建 spatial 视图
spatial = vc.add_view(cm.SPATIAL, dataset=dataset, props={"cellRadius": 100, "fill": "Leiden", "fillOpacity": 1})


scatterplot = vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping="UMAP", props={"xAxisColumn": "0", "yAxisColumn": "1"})
cell_sets = vc.add_view(cm.OBS_SETS, dataset=dataset)
genes = vc.add_view(cm.FEATURE_LIST, dataset=dataset)
heatmap = vc.add_view(cm.HEATMAP, dataset=dataset)
vc.layout((scatterplot | (cell_sets / genes)) / heatmap)
vc.layout(
    (spatial | (scatterplot | (cell_sets / genes))) / heatmap
)
config_dict = vc.export(to='files', base_url='http://localhost:3000', out_dir='./test')
vitessce_url = "http://vitessce.io/?url=data:," + quote_plus(json.dumps(config_dict))
import webbrowser

webbrowser.open(vitessce_url)

I do not know why the "spatial" graph not showing up in the browser

[d5423197]

I dont even know how to debug this. Any help will be appreciated. Btw, Umap, heatmap and gene list are showing up. And when I hover on the heatmap or umap, I can see the coordinate line in the spatial plot. But the spatial plot is all black.

[d5423197]

@keller-mark Hi there, please give me some tips when you have a moment.

[keller-mark]

Hi, there is no spatial information specified within the adding-data part of the configuration. For example, you have not added an image file or specified spatial coordinates within the AnnData object

[d5423197]

@keller-mark hi there, I dont have the image file for now. I just wanna show the spatial info for now. I think this is possible because I saw this in the demo (the spatial plot in http://vitessce.io/#?dataset=eng-2019). Could you please tell me how to achieve that? I thought the spatial coordinate has been specified by obs_locations_path="obsm/spatial"