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Update spatial geometries vignette #143

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merged 5 commits into from
Jan 3, 2024
Merged

Update spatial geometries vignette #143

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9025e7b
Merge pull request #140 from jiajic/dev
jiajic Jan 3, 2024
de99178
Update spatial_geometries.Rmd
jiajic Jan 3, 2024
0103f65
Merge branch 'dev' of https://github.com/jiajic/GiottoClass into dev
jiajic Jan 3, 2024
8995e18
Merge branch 'drieslab:dev' into dev
jiajic Jan 3, 2024
0e8e852
Merge pull request #142 from jiajic/dev
jiajic Jan 3, 2024
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8 changes: 5 additions & 3 deletions vignettes/spatial_geometries.Rmd
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Expand Up @@ -168,10 +168,12 @@ gpoly <- calculateOverlap(gpoly, gimg, verbose = FALSE, progress = FALSE)
Overlaps are stored as a `list` under the `giottoPolygon` `overlaps` slot,
separated by modalities. This list can be retrieved using `overlaps()`.
In the case of overlapped points geometries, the list items are points `SpatVector`
objects. The `poly_ID` column tracks which
objects. The `poly_ID` column tracks which polygon is overlapping the point
feature as designated by `feat_ID` and `feat_ID_uniq`. `NA` values mean that
the feature was not overlapped.

For overlaps intensities, the results are `data.tables` in a nested
list called `intensities`
For overlaps intensities, the results are stored as `data.tables` in a nested
`list` called `intensity` under the main `overlaps` `list`.
```{r}
print(gpoly@overlaps$rna)
print(gpoly@overlaps$intensity)
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