gsource: analyzeData + network refactor + accessor cleanup

.Rbuildignore

@@ -8,5 +8,6 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+test
 ^\.positai$
 ^\.claude$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite Object Definitions and Framework
-Version: 0.5.1
+Version: 0.6.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -40,16 +40,17 @@ Imports:
     matrixStats (>= 0.55.0),
     methods,
     reticulate (>= 1.25),
+    ScaledMatrix,
     stats,
     terra (>= 1.8-21)
 Suggests:
     Biobase,
-    chihaya,
     DelayedArray,
     DelayedMatrixStats (>= 1.24.0),
     exactextractr,
     geometry,
     GiottoData,
+    GiottoDisk,
     HDF5Array (>= 1.18.1),
     knitr,
     magick,
@@ -63,7 +64,6 @@ Suggests:
     rmarkdown,
     RTriangle (>= 1.6-0.10),
     S4Vectors,
-    ScaledMatrix,
     scattermore,
     Seurat,
     SeuratObject,

NAMESPACE

@@ -1,10 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(.DollarNames,affine2d)
+S3method(.DollarNames,analyzeParam)
 S3method(.DollarNames,dimObj)
+S3method(.DollarNames,filterParam)
 S3method(.DollarNames,giotto)
 S3method(.DollarNames,metaData)
 S3method(.DollarNames,processParam)
+S3method(.DollarNames,reduceParam)
 S3method(.DollarNames,spatEnrObj)
 S3method(.DollarNames,spatLocsObj)
 S3method(.DollarNames,terraVectData)
@@ -18,7 +21,6 @@ S3method(print,ghistory)
 S3method(print,ghistory_item)
 S3method(print,giottoInstructions)
 S3method(t,spatLocsObj)
-S3method(t,spatialNetworkObj)
 S3method(utils::head,giottoBinPoints)
 S3method(utils::tail,giottoBinPoints)
 export(addCellMetadata)
@@ -39,6 +41,7 @@ export(aggregateStacksExpression)
 export(aggregateStacksLocations)
 export(aggregateStacksPolygonOverlaps)
 export(aggregateStacksPolygons)
+export(analyzeData)
 export(anndataToGiotto)
 export(annotateGiotto)
 export(annotateSpatialGrid)
@@ -70,8 +73,6 @@ export(compatible_spatial_network)
 export(convHull)
 export(convertGiottoLargeImageToMG)
 export(convert_mgImage_to_array_DT)
-export(convert_to_full_spatial_network)
-export(convert_to_reduced_spatial_network)
 export(cor_flex)
 export(createBentoAdata)
 export(createCellMetaObj)
@@ -104,22 +105,17 @@ export(createSpatialNetwork)
 export(createSpatialWeightMatrix)
 export(create_average_DT)
 export(create_average_detection_DT)
-export(create_cell_meta_obj)
 export(create_cluster_matrix)
-export(create_dim_obj)
-export(create_feat_meta_obj)
-export(create_nn_net_obj)
-export(create_spat_enr_obj)
 export(create_spat_grid_obj)
-export(create_spat_locs_obj)
-export(create_spat_net_obj)
 export(cropGiottoLargeImage)
+export(delaunayNetworkParam)
 export(distGiottoImage)
 export(edge_distances)
 export(estimateImageBg)
 export(evaluate_input)
 export(fDataDT)
 export(featureNetwork)
+export(filterData)
 export(gefToGiotto)
 export(getCellMetadata)
 export(getDimReduction)
@@ -156,6 +152,7 @@ export(giottoToSpatialExperiment)
 export(hexVertices)
 export(installGiottoEnvironment)
 export(joinGiottoObjects)
+export(kNNNetworkParam)
 export(list_cell_id_names)
 export(list_cell_metadata)
 export(list_dim_reductions)
@@ -189,6 +186,7 @@ export(minRect)
 export(my_arowMeans)
 export(my_growMeans)
 export(my_rowMeans)
+export(networkParam)
 export(nnDT_to_kNN)
 export(objHistory)
 export(ometif_metadata)
@@ -217,13 +215,15 @@ export(reconnectGiottoImage)
 export(reconnect_giottoImage_MG)
 export(reconnect_giottoLargeImage)
 export(rectVertices)
+export(reduceData)
 export(removeCellAnnotation)
 export(removeFeatAnnotation)
 export(removeGiottoEnvironment)
 export(replaceGiottoInstructions)
 export(rescalePolygons)
 export(rowMeans_flex)
 export(rowSums_flex)
+export(sNNNetworkParam)
 export(saveGiotto)
 export(setCellMetadata)
 export(setDimReduction)
@@ -292,21 +292,30 @@ export(updateGiottoPointsObject)
 export(updateGiottoPolygonObject)
 export(update_giotto_params)
 export(writeGiottoLargeImage)
+exportClasses(NNNetworkParam)
 exportClasses(affine2d)
+exportClasses(analyzeParam)
 exportClasses(cellMetaObj)
+exportClasses(delaunayNetworkParam)
 exportClasses(dimObj)
 exportClasses(exprObj)
 exportClasses(featMetaObj)
 exportClasses(featureNetwork)
+exportClasses(filterParam)
 exportClasses(giotto)
 exportClasses(giottoBinPoints)
 exportClasses(giottoImage)
 exportClasses(giottoLargeImage)
 exportClasses(giottoPoints)
 exportClasses(giottoPolygon)
+exportClasses(kNNNetworkParam)
+exportClasses(networkParam)
 exportClasses(nnNetObj)
+exportClasses(overlapInfo)
 exportClasses(overlapPointDT)
 exportClasses(processParam)
+exportClasses(reduceParam)
+exportClasses(sNNNetworkParam)
 exportClasses(spatEnrObj)
 exportClasses(spatLocsObj)
 exportClasses(spatialGridObj)

NEWS.md

@@ -1,3 +1,62 @@
+# GiottoClass 0.6.0
+
+## new
+
+- `giotto` class gains a `source` slot for attaching a `gsource`-inheriting
+  backend manager (see {GiottoDisk}).
+- `createGiottoObject()` gains a `backend` param: accepts a filepath or a
+  `gsource` object.
+    - filepath is converted to a `GiottoDisk::gDirSource` automatically.
+    - if `backend = NULL` -- the usual in-memory path is used.
+- `saveGiotto()` and `loadGiotto()` now delegate to
+  `GiottoDisk::snapshotSave()` / `GiottoDisk::snapshotLoad()` when a
+  `gsource` backend is attached to the object. `foldername` and `dir` params
+  are ignored in that case.
+- On-disk persistence via `GiottoDisk::sourceWrite()` is now triggered inside
+  `set_expression_values()`, `set_polygon_info()`, and `set_feature_info()`
+  when a `gsource` backend is present.
+- `createNetwork()` is now an S4 generic with method dispatch on
+  `matrix`, `spatLocsObj`, `dimObj`, and `giotto` inputs.
+- `networkParam` virtual class with concrete constructors
+  `kNNNetworkParam()`, `sNNNetworkParam()`, and `delaunayNetworkParam()`
+  configure `createNetwork()` calls. The legacy `type` string arg is
+  superseded by passing a `*NetworkParam` object.
+
+## changes
+
+- `h5_file` param in `createGiottoObject()` is deprecated; use `backend`
+  instead.
+- `overlapInfo` class exported as an extension point.
+- `updateGiottoObject()` now upgrades pre-0.6.0 objects to initialize the
+  new `source` slot, and migrates `spatialNetworkObj` / `nnNetObj` to the
+  new igraph-based storage (see breaking changes).
+- `createNearestNetwork()`, `createSpatialDelaunayNetwork()`, and
+  `createSpatialKNNnetwork()` are now thin wrappers over `createNetwork()`.
+  Behavior is preserved.
+
+## breaking changes
+
+- Network subobject storage migrated from `data.table` to `igraph`:
+    - `spatialNetworkObj`: `@networkDT` → `@network` (igraph),
+      `@networkDT_before_filter` → `@unfiltered` (igraph)
+    - `nnNetObj`: `@igraph` → `@network`
+    - `updateGiottoObject()` migrates serialized pre-0.6.0 objects. The
+      same migration runs on-load via `initialize()` so legacy subobjects
+      passed to setters (`setSpatialNetwork()`, `setNearestNetwork()`)
+      are upgraded transparently.
+- `getSpatialNetwork()` `output` choices changed:
+  `"networkDT_before_filter"` → `"unfiltered"`; new option `"igraph"`
+  returns the underlying graph directly.
+- Removed exported helpers `convert_to_full_spatial_network()` and
+  `convert_to_reduced_spatial_network()`. The edge table is now an
+  igraph; use `igraph::as_data_frame(net, what = "edges")` if a
+  data.table form is needed.
+- Geometric-transform methods (`flip()`, `spatShift()`, `t()`, `spin()`,
+  `rescale()`, `affine()`) are no longer defined on `spatialNetworkObj`.
+  Graph topology is invariant under these transforms; gobject-level
+  walkers skip the spatial-network slot.
+
+
 # GiottoClass 0.5.1 (2026/05/14)
 
 ## changes