Merge branch 'drieslab:suite_dev' into suite_dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.6
+Version: 4.0.9
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -27,11 +27,11 @@ URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.1
 Depends:
-    base (>= 3.5.0),
-    utils (>= 3.5.0),
-    R (>= 3.5.0),
+    base (>= 4.1.0),
+    utils (>= 4.1.0),
+    R (>= 4.1.0),
     methods,
-    GiottoClass (>= 0.3.0)
+    GiottoClass (>= 0.3.1)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -41,12 +41,12 @@ Imports:
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
     ggrepel,
-    GiottoUtils (>= 0.1.7),
-    GiottoVisuals (>= 0.2.0),
+    GiottoUtils (>= 0.1.9),
+    GiottoVisuals (>= 0.2.2),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
-    Matrix (>= 1.6.2),
+    Matrix (>= 1.6-2),
     MatrixGenerics,
     plotly,
     progressr,

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,combIcfObject)
+S3method(print,icfObject)
 export("%>%")
 export("activeFeatType<-")
 export("activeSpatUnit<-")
@@ -145,13 +147,12 @@ export(create_jackstrawplot)
 export(create_screeplot)
 export(crop)
 export(cropGiottoLargeImage)
-export(crossSectionGenePlot)
-export(crossSectionGenePlot3D)
+export(crossSectionFeatPlot)
+export(crossSectionFeatPlot3D)
 export(crossSectionPlot)
 export(crossSectionPlot3D)
 export(detectSpatialCorFeats)
 export(detectSpatialCorFeatsMatrix)
-export(detectSpatialCorGenes)
 export(detectSpatialPatterns)
 export(dimCellPlot)
 export(dimCellPlot2D)
@@ -258,7 +259,7 @@ export(heatmSpatialCorGenes)
 export(hexVertices)
 export(hyperGeometricEnrich)
 export(initHMRF_V2)
-export(insertCrossSectionGenePlot3D)
+export(insertCrossSectionFeatPlot3D)
 export(insertCrossSectionSpatPlot3D)
 export(installGiottoEnvironment)
 export(instructions)

NEWS.md

@@ -1,3 +1,40 @@
+# Giotto 4.0.10 TBD
+
+## Bug fixes
+* Fix error in `plotInteractivePolygons()` when providing a spatial plot with a continuous scale [#964](https://github.com/drieslab/Giotto/issues/964) by jweis3
+* Fix error in DWLS `find_dampening_constant()` when `S[subset, ]` produces only 1 gene.
+
+# Giotto 4.0.9
+
+## Breaking changes
+* Deprecated `detectSpatialCorGenes()` removed. Use `detectSpatialCorFeats()` instead
+* Deprecated `findInteractionChangedGenes()` removed. Use `findInteractionChangedFeats()` instead
+* Deprecated `findCellProximityGenes()` removed. Use `findInteractionChangedFeats()` instead
+
+## Bug fixes
+* Add catch in `runPCAprojectionBatch()` for when ncp requested exceeds number of feats used
+* Make `spatCellCellcom()` respect `verbose` flag [#949](https://github.com/drieslab/Giotto/issues/949) by rbutleriii
+
+## Enhancements
+* `print()` methods for `icfObject` and `combIcfObject`
+
+## Changes
+* require GiottoUtils (>= 0.1.9)
+
+# Giotto 4.0.8 (2024/05/22)
+
+## Breaking changes
+* `crossSectionGenePlot()` removed. Use `crossSectionFeatPlot()` instead
+* `crossSectionGenePlot3D()` removed. Use `crossSectionFeatPlot3D()` instead
+* `insertCrossSectionGenePlot3D()` removed Use `insertCrossSectionFeatPlot3D()` instead
+
+## Bug fixes
+* `binSpect()` param passing error introduced in _v4.0.6_
+* updated `viewHMRFresults3D()` and `viewHMRFresults2D()`
+* updated `createCrossSections()`, `insertCrossSectionSpatPlot3D()`, `crossSectionPlot()`, `crossSectionFeatPlot3D()`, `insertCrossSectionFeatPlot3D()`, `crossSectionPlot3D()`, `crossSectionFeatPlot()`
+
+## Changes
+* GiottoVisuals (>= 0.2.2), GiottoClass (>= 0.3.1), GiottoUtils (>= 0.1.8) are now required.
 
 # Giotto 4.0.6 (2024/05/13)