Restore Bioconductor-compatible QScore APIs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpaceTrooper
 Type: Package
 Title: SpaceTrooper performs Quality Control analysis of Image-Based spatial
-Version: 1.1.8
+Version: 1.1.9
 Authors@R:
         c(person("Dario", "Righelli",
             email="dario.righelli@gmail.com",
@@ -23,7 +23,7 @@ Description: SpaceTrooper performs Quality Control analysis using data driven
 License: MIT + file LICENSE
 Encoding: UTF-8
 Depends: 
-    R (>= 4.4.0),
+    R (>= 4.6.0),
     SpatialExperiment
 Imports:
     DropletUtils,

NAMESPACE

@@ -1,18 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
-export(.applyQScoreModel)
 export(.getActiveGeometryName)
 export(.renameGeometry)
 export(.setActiveGeometry)
 export(addPolygonsToSPE)
+export(applyQCScoreModel)
+export(applyQScoreModel)
 export(checkOutliers)
 export(computeAreaFromPolygons)
 export(computeAspectRatioFromPolygons)
 export(computeCenterFromPolygons)
 export(computeLambda)
 export(computeMissingMetricsMerfish)
 export(computeMissingMetricsXenium)
+export(computeOutliersQCScore)
 export(computeOutliersQScore)
+export(computeQCScore)
+export(computeQCScoreFlags)
 export(computeQScore)
 export(computeQScoreFlags)
 export(computeSpatialOutlier)
@@ -132,3 +136,4 @@ importFrom(stats,complete.cases)
 importFrom(stats,model.matrix)
 importFrom(stats,predict)
 importFrom(stats,quantile)
+importFrom(stats,terms)

NEWS.md

@@ -1,8 +1,38 @@
-# Changes in version 1.1.8
-
-* implementing Quality Score computation with custom formula
-* fixing naming of spacetrooper utilities vignette
-* adding citation file with biorxiv paper
+# Changes in version 1.1.9
+
+* Added the canonical `computeQScore()`, `computeQScoreFlags()`,
+  `computeOutliersQScore()`, and `applyQScoreModel()` APIs.
+* Retained `computeQCScore()`, `computeQCScoreFlags()`,
+  `computeOutliersQCScore()`, and `applyQCScoreModel()` as deprecated
+  compatibility APIs. They preserve historical arguments, `QC_score`,
+  `low_qcscore`, `low_threshold_qcscore`, and `QCScore_model*` metadata.
+* Restored historical plotting arguments (`size`, `alpha`, `alphaNumbers`,
+  `csize`, `calpha`, `mapNumbersCol`, and `mapAlphaNumbers`) as aliases for
+  the canonical plotting arguments. Canonical arguments take precedence when
+  both forms are supplied.
+* Restored `getModelFormula(formulaVars, verbose=FALSE)` compatibility while
+  accepting `metricList` as a named replacement.
+* Restored the public `computeLambda(trainDF, modelFormula)` signature,
+  complete-case filtering, and support for both `qcscore_train` and
+  `QScore_train`.
+* User-supplied `modelFormula` values are now fitted without adding, removing,
+  or rebuilding terms. Supported subsets, additive formulas, and selected
+  interactions are preserved.
+* Supported base QC metrics selected by a custom `modelFormula` now determine
+  the outliers, good and bad cells, and `QScore_train` used for model training;
+  omitted metrics no longer contribute to training-label construction.
+* Formula predictors are limited to `log2SignalDensity`, `Area_um`,
+  `log2AspectRatio`, and `log2Ctrl_total_ratio`. Unsupported predictors and
+  transformations now produce informative errors, and CosMx-only border terms
+  are checked against dataset technology.
+* Model transfer now has a canonical public API, preserves training matrix
+  column order, supports validated custom formulas, and retains the historical
+  deprecated interface.
+* Fixed the SpaceTrooper utilities vignette name and added the bioRxiv
+  citation.
+* Follow-up: intercept handling remains unchanged in this release and should be
+  reviewed consistently across training, lambda selection, prediction, and
+  model transfer.
 
 # Changes in version 1.1.7