The clustering
workflow accepts both cell suspension datasets and spatial transcriptomics data as input that have been ingested with the qc_spatial
workflow and optionally filtered with the spatial_preprocess
workflow.
The workflow expects a single MuData
object with the spatial data saved in mdata.mod["spatial"]
.
Set spatial: True
in the configuration file and customize the spatial modality clustering parameters exactly as you would for a single cell experiment. For more information check the clustering workflow