Comments (1)
lambdamoses
commented on May 26, 2024
Maybe. Voyager actually doesn't replace everything that Seurat and Giotto do. Because SFE is based on SCE, I don't need to reimplement the non-spatial EDA functionalities in Seurat and Giotto because scater and scran already have the functionalities. It's more like bringing the geospatial tradition to the SCE ecosystem. Seurat itself doesn't do much in spatial analyses. Giotto at present has some methods for categorical spatial data that Voyager doesn't have. Since Bioconductor doesn't allow dependencies that are not on CRAN or Bioconductor, it would not be possible to incorporate many methods into Voyager. But I wish that more people take interoperability seriously so it won't be necessary to incorporate the methods.
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Related Issues (20)
- Polygon boundaries showing despite linewidth = 0 in `plotSpatialFeature` on Windows
- Plot rowGeometries HOT 8
- Matrix >= 1.6.2 breaks Voyager HOT 2
- Error when bbox is used HOT 3
- Refactor `SFEMethods` to be more like `BlusParam`
- Specify whether bivariate method in `SFEMethod` class is symmetric
- Plot multiple grayscale images at once as different channels in `plotSpatialFeature` and related functions
- Allow users to select any channel in images in plotting functions
- Option to plot image in a separate adjacent panel rather than behind cells/spots
- Option to plot only polygon outlines without fill in `plotColGeometry`
- Plot scale bar when unit = "micron"
- Write alt text for vignette figures
- Vignette using multiple samples
- Support `BioFormatsImage` and `EBImage` in `plotSpatialFeature` HOT 1
- Vignette for Tomo-seq
- Add argument to `plotSpatialFeature` for whether to show axes
- Plotting function just to show images without geometries
- Joint count vignette
- Vignette about multi-scale analyses
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