Update Image-based Spatial Vignette in Seurat v.5.5.0#10379
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YoukaiFromAccounting wants to merge 2 commits into
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Update Image-based Spatial Vignette in Seurat v.5.5.0#10379YoukaiFromAccounting wants to merge 2 commits into
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Pull request overview
Updates the image-based spatial vignette to align with the Seurat v5.5.0 CRAN release by adjusting future globals settings to avoid knit-time memory errors and removing an outdated Xenium Human Lung example section.
Changes:
- Set
options(future.globals.maxSize = 10 * 1024^3)near the vignette initialization to raise the allowed exported globals size forfuture. - Removed the “Human Lung: 10x Genomics Xenium In Situ” vignette section.
- Removed the now-redundant per-section
future.globals.maxSizeoverride in the Nanostring integration chunk.
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Minor changes to seurat5_spatial_vignette_2.Rmd to update vignette with the release of Seurat v5.5.0 to CRAN. Changes include:
-Increasing future.globals.maxSize to 10GB (otherwise run into memory usage errors during vignette knitting)
-Removing outdated Human Lung 10x Genomics example