binned points structure for sequencing-based technologies

DESCRIPTION

@@ -80,13 +80,20 @@ Suggests:
 Remotes: drieslab/GiottoUtils
 Config/testthat/edition: 3
 Collate: 
+    'classes-virtuals.R'
+    'classes-utils.R'
+    'classes-images.R'
+    'classes-overlaps.R'
+    'classes-points.R'
+    'classes-polygons.R'
     'package_imports.R'
     'classes.R'
     'generics.R'
     'NN_network.R'
     'aggregate.R'
     'auxilliary.R'
     'buffer.R'
+    'classes-binpoints.R'
     'combine_metadata.R'
     'slot_accessors.R'
     'create.R'

NAMESPACE

@@ -11,6 +11,7 @@ S3method(.DollarNames,terraVectData)
 S3method(as.data.frame,overlapIntensityDT)
 S3method(as.data.frame,overlapPointDT)
 S3method(as.data.table,SpatVector)
+S3method(as.data.table,giottoBinPoints)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
 S3method(print,ghistory)
@@ -75,6 +76,7 @@ export(createCellMetaObj)
 export(createDimObj)
 export(createExprObj)
 export(createFeatMetaObj)
+export(createGiottoBinPoints)
 export(createGiottoImage)
 export(createGiottoInstructions)
 export(createGiottoLargeImage)
@@ -295,6 +297,7 @@ exportClasses(exprObj)
 exportClasses(featMetaObj)
 exportClasses(featureNetwork)
 exportClasses(giotto)
+exportClasses(giottoBinPoints)
 exportClasses(giottoImage)
 exportClasses(giottoLargeImage)
 exportClasses(giottoPoints)
@@ -353,6 +356,7 @@ exportMethods(ext)
 exportMethods(featIDs)
 exportMethods(featType)
 exportMethods(flip)
+exportMethods(head)
 exportMethods(hist)
 exportMethods(hull)
 exportMethods(instructions)
@@ -381,6 +385,7 @@ exportMethods(splitGeom)
 exportMethods(subset)
 exportMethods(symdif)
 exportMethods(t)
+exportMethods(tail)
 exportMethods(union)
 exportMethods(vect)
 exportMethods(wrap)
@@ -429,6 +434,7 @@ importMethodsFrom(terra,density)
 importMethodsFrom(terra,erase)
 importMethodsFrom(terra,ext)
 importMethodsFrom(terra,flip)
+importMethodsFrom(terra,head)
 importMethodsFrom(terra,hist)
 importMethodsFrom(terra,hull)
 importMethodsFrom(terra,intersect)
@@ -441,6 +447,7 @@ importMethodsFrom(terra,snap)
 importMethodsFrom(terra,spin)
 importMethodsFrom(terra,symdif)
 importMethodsFrom(terra,t)
+importMethodsFrom(terra,tail)
 importMethodsFrom(terra,union)
 importMethodsFrom(terra,vect)
 importMethodsFrom(terra,wrap)

NEWS.md

@@ -2,13 +2,18 @@
 
 ## changes
 - `calculateOverlap()` and `overlapToMatrix()` param harmonization
+- refactor of `saveGiotto()` and `loadGiotto()`
+- code reorganization for `classes.R`
 
 ## new
-- `aggregateFeatures()` wrapper for running `calculateOverlap()` and `overlapToMatrix()`
+- `aggregateFeatures()` giotto object wrapper function for running `calculateOverlap()` and `overlapToMatrix()`
 - `overlapPointDT()` and `overlapIntensityDT()` classes to store overlaps relationships efficiently and help with aggregation pipeline
+- `giottoBinPoints` class for efficient binned spatial points
 
 ## bug fixes
 - `overlaps()` will now properly find image overlaps
+- fix a naming bug when exporting images during save
+
 
 
 # GiottoClass 0.4.12 (2025/12/12)

R/aggregate.R

@@ -1,5 +1,6 @@
 # collate
 #' @include generics.R
+#' @include classes.R
 NULL
 
 # aggregate expression ####
@@ -802,6 +803,7 @@ setMethod(
             )
         )
 
+        # (constructor) see classes-overlaps.R
         .create_overlap_point_dt(x, y, res, feat_ids = feat_ids)
     }
 )
@@ -988,87 +990,7 @@ calculateOverlapRaster <- function(
     }
 }
 
-#' @param overlap_data `data.table` of extracted intensity values per poly_ID
-#' @noRd
-.create_overlap_intensity_dt <- function(overlap_data) {
-    odt <- new("overlapIntensityDT", data = overlap_data)
-    odt@nfeats <- ncol(overlap_data) - 1L
-    odt
-}
-
-#' @param x from data (SpatVector)
-#' @param y to data (SpatVector)
-#' @param overlap_data relationships (data.frame). Expected to be numeric row
-#' indices between x and y
-#' @param keep additional col(s) in `y` to keep
-#' @noRd
-.create_overlap_point_dt <- function(x, y,
-        overlap_data, keep = NULL, feat_ids) {
-    poly <- feat_idx <- feat <- feat_id_index <- NULL # NSE vars
-    # cleanup input overlap_data
-    checkmate::assert_data_frame(overlap_data)
-    data.table::setDT(overlap_data)
-    cnames <- colnames(overlap_data)
-    data.table::setnames(overlap_data,
-        old = c(cnames[[2]], cnames[[1]]),
-        new = c("poly", "feat_idx")
-    )
-    # make relationships table sparse by removing non-overlapped features
-    # these results are indexed by all features, so no need to filter
-    # non-overlapped polys
-    overlap_data <- overlap_data[!is.na(poly)]
-
-    # extract needed info from y
-    keep <- c("feat_ID", "feat_ID_uniq", keep)
-    ytab <- terra::as.data.frame(y[overlap_data$feat_idx, keep])
-
-    # initialize overlap object and needed ids
-    sids <- x$poly_ID
-    fids <- unique(ytab$feat_ID)
-    odt <- new("overlapPointDT",
-        spat_ids = sids,
-        feat_ids = feat_ids,
-        nfeats = as.integer(nrow(y))
-    )
-
-    # Ensure data is stored as integer or integer-based mapping
-    ## - if poly/feat_idx contents are NOT integer coercible, establish a map #
-    if (!overlap_data[, checkmate::test_integerish(head(poly, 100))]) {
-        overlap_data[, poly := match(poly, sids)]
-    }
-    if (!overlap_data[, checkmate::test_integerish(head(feat_idx, 100))]) {
-        overlap_data[, feat_idx := match(feat_idx, fids)]
-    }
-    ## -- if still not integer, coerce to integer --------------------------- #
-    if (!is.integer(overlap_data$poly[1])) {
-        overlap_data[, poly := as.integer(poly)]
-    }
-    if (!is.integer(overlap_data$feat_idx[1])) {
-        overlap_data[, feat_idx := as.integer(feat_idx)]
-    }
 
-    # append y attribute info
-    overlap_data <- cbind(overlap_data, ytab)
-    data.table::setnames(overlap_data,
-        old = c("feat_ID_uniq", "feat_ID"),
-        new = c("feat", "feat_id_index")
-    )
-    if (!is.integer(overlap_data$feat[1])) {
-        overlap_data[, feat := as.integer(feat)]
-    }
-    # add feat_ID map
-    overlap_data[, feat_id_index := match(feat_id_index, odt@feat_ids)]
-    # remove feat_idx which may not be reliable after feature subsets
-    overlap_data[, feat_idx := NULL]
-    # set indices
-    data.table::setkeyv(overlap_data, "feat")
-    data.table::setindexv(overlap_data, "poly")
-    data.table::setcolorder(overlap_data, c("poly", "feat", "feat_id_index"))
-    # add to object
-    odt@data <- overlap_data
-
-    odt
-}