Merge pull request #1110 from jiajic/process_data

Feat: new (post-filtering) composable data processing and pipelining

NAMESPACE

@@ -3,6 +3,9 @@
 S3method(.DollarNames,CosmxReader)
 S3method(.DollarNames,VisiumHDReader)
 S3method(.DollarNames,XeniumReader)
+S3method(.DollarNames,adjustParam)
+S3method(.DollarNames,normParam)
+S3method(.DollarNames,scaleParam)
 export("%>%")
 export("activeFeatType<-")
 export("activeSpatUnit<-")
@@ -38,6 +41,7 @@ export(addSpatialCentroidLocationsLayer)
 export(addStatistics)
 export(addVisiumPolygons)
 export(adjustGiottoMatrix)
+export(adjustParam)
 export(aggregateStacks)
 export(aggregateStacksExpression)
 export(aggregateStacksLocations)
@@ -286,6 +290,7 @@ export(makeSignMatrixDWLSfromMatrix)
 export(makeSignMatrixPAGE)
 export(makeSignMatrixRank)
 export(mergeClusters)
+export(normParam)
 export(normalizeGiotto)
 export(objHistory)
 export(objName)
@@ -337,6 +342,7 @@ export(polyStamp)
 export(preprocessImageToMatrix)
 export(print.combIcfObject)
 export(print.icfObject)
+export(processExpression)
 export(processGiotto)
 export(prov)
 export(rankSpatialCorGroups)
@@ -394,6 +400,7 @@ export(sankeyRelate)
 export(sankeySet)
 export(sankeySetAddresses)
 export(saveGiotto)
+export(scaleParam)
 export(screePlot)
 export(selectPatternGenes)
 export(setCellMetadata)
@@ -523,6 +530,7 @@ import(ggplot2)
 import(methods)
 import(stats, except = density)
 import(utils)
+importClassesFrom(Matrix,Matrix)
 importClassesFrom(data.table,data.table)
 importFrom(GiottoClass,"activeFeatType<-")
 importFrom(GiottoClass,"activeSpatUnit<-")

NEWS.md

@@ -14,6 +14,10 @@
 * `importCosMx()` now supports vectors of filepaths when provided to `$load_images()` and `$load_polys()`
 * `importCosMx()` Selected FOVs are now selected in `plot()`.
 
+## New
+* `processExpression()` for `giotto` implemented via the `processData()` framework in {GiottoClass} v0.4.7 (see `?processData` and `?process_param`)
+* `L2` and `TF-IDF` normalization methods accessible via the `processData()` framework
+
 # Giotto 4.2.0 (2025/01/17)
 
 ## Breaking Changes