Make CellTrek compatible with Seurat v5 (5.3.0) - #48
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- Replace direct assay-slot access (@data/@counts/@scale.data) with version-agnostic GetAssayData()/SetAssayData() across celltrek.R, scoexp.R, FindCorMarkers.R
- Make DimReduc keys v5-compliant (celltrek_/pca_/umap_/tsne_)
- Read ST coordinates via GetTissueCoordinates() (VisiumV1 + VisiumV2/FOV); guard image@coordinates writes to VisiumV1
- Add traint(coord_df=) to supply spatial coordinates directly and bypass image-structure/naming differences (errors clearly if unresolved)
- Switch interpolation dependency akima -> interp (DESCRIPTION/NAMESPACE)
- Update README tutorial code for v5 (HVFInfo, GetAssayData)
- Add local functional tests and result figures; bump version to 0.0.95
- Replace direct assay-slot access (@data/@counts/@scale.data) with version-agnostic GetAssayData()/SetAssayData() across celltrek.R, scoexp.R, FindCorMarkers.R - Make DimReduc keys v5-compliant (celltrek_/pca_/umap_/tsne_) - Read ST coordinates via GetTissueCoordinates() (VisiumV1 + VisiumV2/FOV); guard image@coordinates writes to VisiumV1 - Add traint(coord_df=) to supply spatial coordinates directly and bypass image-structure/naming differences (errors clearly if unresolved) - Switch interpolation dependency akima -> interp (DESCRIPTION/NAMESPACE) - Update README tutorial code for v5 (HVFInfo, GetAssayData) - Add local functional tests and result figures; bump version to 0.0.95 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
GetTissueCoordinates() rescales VisiumV1 coordinates by the image scale factor (~5.8x smaller), which shrank spot distances and made the fixed repel_r over-disperse the charting into a uniform blob. traint() now prefers the image @coordinates[,coord_xy] slot (VisiumV1, original scale) and only falls back to GetTissueCoordinates() for classes lacking it (VisiumV2/FOV). Verified on both VisiumV1 (brain) and VisiumV2 (stxBrain). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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