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Change: Updates to aggregation #300

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Merged
jiajic merged 55 commits into from
Dec 31, 2025
Merged

Change: Updates to aggregation #300

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78a314b
aggregateFeatures and aggregation changes
jiajic Mar 13, 2025
21f2f78
enh: improve exprObj show() methods
jiajic Apr 3, 2025
44cb004
fix: revert to previous flip handling for images
jiajic Apr 7, 2025
87ee8ba
chore: remove unused flip image internal
jiajic Apr 7, 2025
749c7b6
enh: tif tool updates
jiajic Apr 24, 2025
a7aee31
feat: aggregation changes
jiajic Apr 30, 2025
c0b072b
chore: docs edits
jiajic Apr 30, 2025
eab9899
chore: move gpoints and gpoly updates in init giotto into updateGiott…
jiajic May 1, 2025
12bd132
update `combineFeatureOverlapData()` to work with new overlap structure
jiajic May 1, 2025
4423677
chore: catch up dev
jiajic May 2, 2025
fae4613
chore: docs
jiajic May 2, 2025
d6eea2c
Merge branch 'dev' of https://github.com/drieslab/GiottoClass into pa…
jiajic May 2, 2025
e6f82e1
fix: scoping on local seed in tests
jiajic May 2, 2025
f9e0017
fix: as.matrix method for points overlaps
jiajic May 2, 2025
0a7823d
enh: make subsetting point overlaps more robust
jiajic May 3, 2025
9e75f3e
enh: dim() and rbind() for point overlaps
jiajic May 3, 2025
bd6c56b
fix: `aggregateStacksPolygonOverlaps()` for new point overlap impleme…
jiajic May 3, 2025
c303535
fix: remove now unecessary handling for overlaps saving
jiajic May 4, 2025
9f654dc
fix: incorrect overlap point feat_id tracking
jiajic May 4, 2025
2630dbb
update: test for new param names
jiajic May 4, 2025
b1be26f
chore: update test expected based on changes
jiajic May 4, 2025
1092a3f
fix: remove unused overlap reading
jiajic May 5, 2025
1feeea2
fix: make overlap reading versioned
jiajic May 5, 2025
7c0ce21
fix: checking logic for overlaps load
jiajic May 5, 2025
a8bbfb6
chore: docs
jiajic May 5, 2025
47e2247
chore: catch up to staging
jiajic May 15, 2025
e18de85
Revert "chore: catch up to staging"
jiajic May 15, 2025
beffc3d
Reapply "chore: catch up to staging"
jiajic May 15, 2025
7b5b01f
chore: catch up to dev
jiajic May 20, 2025
20562b8
chore: remove unused line
jiajic May 20, 2025
98402e3
Merge branch 'dev' of https://github.com/drieslab/GiottoClass into pa…
jiajic Jun 16, 2025
0670056
chore: docs
jiajic Jun 16, 2025
01e16ab
ci: update
jiajic Jun 16, 2025
b786fbe
enh: ncol and nrow for new overlap objects
jiajic Jun 16, 2025
e5cdacc
chore: conflict
jiajic Jun 16, 2025
43c6e56
enh: df coercion for overlapIntesityDT
jiajic Jun 16, 2025
70ef2ab
chore: improve docs for utility class
jiajic Jun 16, 2025
bb68a1e
Merge branch 'dev' into patch_agg_feats
jiajic Jul 7, 2025
a2dd359
Merge branch 'dev' into patch_agg_feats
jiajic Sep 22, 2025
386c6b8
chore: catch up to dev
jiajic Nov 11, 2025
aa55408
catchup and fix conflict
jiajic Dec 19, 2025
e19c090
change: overlap handling during gpoly rbind
jiajic Dec 19, 2025
4b43b24
change: default point overlap method -> vector
jiajic Dec 19, 2025
776324e
chore: docs
jiajic Dec 19, 2025
aa15e9c
fix test for new vector overlap default
jiajic Dec 22, 2025
df09a05
fix: raster aggregate count col
jiajic Dec 28, 2025
55393be
fix: aggregation testing: points count gen
jiajic Dec 28, 2025
e9e8367
chore: reorganize for clarity
jiajic Dec 28, 2025
6149adb
refactor: point extraction
jiajic Dec 30, 2025
6cfd6fd
chore: update tests
jiajic Dec 30, 2025
475daa5
fixes
jiajic Dec 31, 2025
55a4253
Update aggregate.R
jiajic Dec 31, 2025
f976dcc
Update test-aggregate.R
jiajic Dec 31, 2025
bc4eebc
chore: docs
jiajic Dec 31, 2025
8bee86a
test fixes
jiajic Dec 31, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: GiottoClass
Title: Giotto Suite Object Definitions and Framework
Version: 0.4.12
Version: 0.5.0
Authors@R: c(
person("Ruben", "Dries", email = "rubendries@gmail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
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4 changes: 4 additions & 0 deletions NAMESPACE
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Expand Up @@ -8,6 +8,8 @@ S3method(.DollarNames,processParam)
S3method(.DollarNames,spatEnrObj)
S3method(.DollarNames,spatLocsObj)
S3method(.DollarNames,terraVectData)
S3method(as.data.frame,overlapIntensityDT)
S3method(as.data.frame,overlapPointDT)
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@coderabbitai coderabbitai bot Jun 16, 2025

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🛠️ Refactor suggestion

Missing symmetrical as.data.frame for overlapIntensityDT

You registered as.data.frame.overlapPointDT, but its sibling class overlapIntensityDT did not get the same treatment. Down-stream code that relies on as.data.frame() for both overlap classes will break.

+S3method(as.data.frame,overlapIntensityDT)

Add the roxygen tag to the method implementation and re-document.

🤖 Prompt for AI Agents 
In the NAMESPACE file at line 11, you registered the S3 method as.data.frame for
overlapPointDT but missed doing the same for overlapIntensityDT. To fix this,
add a corresponding S3method(as.data.frame, overlapIntensityDT) line to the
NAMESPACE file. Also, in the R script where the as.data.frame.overlapIntensityDT
method is defined, add the appropriate roxygen2 @method tag for as.data.frame
and overlapIntensityDT, then re-document the package to update the NAMESPACE
accordingly.

S3method(as.data.table,SpatVector)
S3method(as.data.table,giottoPoints)
S3method(as.data.table,giottoPolygon)
Expand All @@ -28,6 +30,7 @@ export(addNetworkLayout)
export(addSpatialCentroidLocations)
export(addSpatialCentroidLocationsLayer)
export(add_img_array_alpha)
export(aggregateFeatures)
export(aggregateStacks)
export(aggregateStacksExpression)
export(aggregateStacksLocations)
Expand Down Expand Up @@ -297,6 +300,7 @@ exportClasses(giottoLargeImage)
exportClasses(giottoPoints)
exportClasses(giottoPolygon)
exportClasses(nnNetObj)
exportClasses(overlapPointDT)
exportClasses(processParam)
exportClasses(spatEnrObj)
exportClasses(spatLocsObj)
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14 changes: 14 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,22 @@
# GiottoClass 0.5.0

## changes
- `calculateOverlap()` and `overlapToMatrix()` param harmonization

## new
- `aggregateFeatures()` wrapper for running `calculateOverlap()` and `overlapToMatrix()`
- `overlapPointDT()` and `overlapIntensityDT()` classes to store overlaps relationships efficiently and help with aggregation pipeline

## bug fixes
- `overlaps()` will now properly find image overlaps


# GiottoClass 0.4.12 (2025/12/12)

## enhancements
- automatic checking for `"count"` column in feature info


## new
- `misc` slot for storing unstructured data

Expand Down
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