Merge branch 'drieslab:suite_dev' into suite_dev

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Spatial Single-Cell Transcriptomics Toolbox
 Version: 4.0.6
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
-		 role = c("aut", "cre")),
+		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
 	person("Jiaji", "George Chen", email = "[email protected]",
 		 role = c("aut")),
 	person("Joselyn C.", "Chávez-Fuentes", email = "[email protected]",
@@ -19,9 +19,8 @@ Authors@R: c(
 	person("Natalie", "Del Rossi", email = "[email protected]",
 		 role = c("aut"))
 	)
-Maintainer: Ruben Dries <[email protected]>
 Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
-License: GPL (>= 3)
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
@@ -32,7 +31,7 @@ Depends:
     utils (>= 3.5.0),
     R (>= 3.5.0),
     methods,
-    GiottoClass (>= 0.2.4)
+    GiottoClass (>= 0.3.0)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -42,8 +41,8 @@ Imports:
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
     ggrepel,
-    GiottoUtils (>= 0.1.6),
-    GiottoVisuals (>= 0.1.1),
+    GiottoUtils (>= 0.1.7),
+    GiottoVisuals (>= 0.2.0),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
@@ -127,10 +126,6 @@ Suggests:
     trendsceek,
     testthat (>= 3.0.0),
     qs
-Remotes:
-    drieslab/GiottoUtils,
-    drieslab/GiottoClass,
-    drieslab/GiottoVisuals
 Collate:
     'auxiliary_giotto.R'
     'cell_segmentation.R'
@@ -164,6 +159,6 @@ Collate:
     'variable_genes.R'
     'wnn.R'
     'zzz.R'
-biocViews:
+biocViews: Software, Technology, Spatial, SingleCell, Transcriptomics
 VignetteBuilder: knitr
 Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Giotto authors

NAMESPACE

@@ -156,6 +156,7 @@ export(detectSpatialPatterns)
 export(dimCellPlot)
 export(dimCellPlot2D)
 export(dimFeatPlot2D)
+export(dimFeatPlot3D)
 export(dimGenePlot3D)
 export(dimPlot)
 export(dimPlot2D)
@@ -429,12 +430,14 @@ export(spatDeconvPlot)
 export(spatDimCellPlot)
 export(spatDimCellPlot2D)
 export(spatDimFeatPlot2D)
+export(spatDimFeatPlot3D)
 export(spatDimGenePlot3D)
 export(spatDimPlot)
 export(spatDimPlot2D)
 export(spatDimPlot3D)
 export(spatFeatPlot2D)
 export(spatFeatPlot2D_single)
+export(spatFeatPlot3D)
 export(spatGenePlot3D)
 export(spatIDs)
 export(spatInSituPlotDensity)
@@ -484,12 +487,13 @@ export(violinPlot)
 export(wrap)
 export(writeGiottoLargeImage)
 export(writeHMRFresults)
+exportMethods(interpolateFeature)
 import(GiottoClass)
 import(GiottoUtils)
 import(GiottoVisuals)
 import(ggplot2)
 import(methods)
-import(stats)
+import(stats, except = density)
 import(utils)
 importClassesFrom(data.table,data.table)
 importFrom(GiottoClass,"activeFeatType<-")
@@ -716,6 +720,7 @@ importFrom(GiottoVisuals,addGiottoImageToSpatPlot)
 importFrom(GiottoVisuals,dimCellPlot)
 importFrom(GiottoVisuals,dimCellPlot2D)
 importFrom(GiottoVisuals,dimFeatPlot2D)
+importFrom(GiottoVisuals,dimFeatPlot3D)
 importFrom(GiottoVisuals,dimGenePlot3D)
 importFrom(GiottoVisuals,dimPlot)
 importFrom(GiottoVisuals,dimPlot2D)
@@ -750,12 +755,14 @@ importFrom(GiottoVisuals,spatDeconvPlot)
 importFrom(GiottoVisuals,spatDimCellPlot)
 importFrom(GiottoVisuals,spatDimCellPlot2D)
 importFrom(GiottoVisuals,spatDimFeatPlot2D)
+importFrom(GiottoVisuals,spatDimFeatPlot3D)
 importFrom(GiottoVisuals,spatDimGenePlot3D)
 importFrom(GiottoVisuals,spatDimPlot)
 importFrom(GiottoVisuals,spatDimPlot2D)
 importFrom(GiottoVisuals,spatDimPlot3D)
 importFrom(GiottoVisuals,spatFeatPlot2D)
 importFrom(GiottoVisuals,spatFeatPlot2D_single)
+importFrom(GiottoVisuals,spatFeatPlot3D)
 importFrom(GiottoVisuals,spatGenePlot3D)
 importFrom(GiottoVisuals,spatInSituPlotDensity)
 importFrom(GiottoVisuals,spatInSituPlotHex)

NEWS.md

@@ -1,9 +1,12 @@
 
-# Giotto 4.0.6
+# Giotto 4.0.6 (2024/05/13)
 
 ## Enhancements
 * New `interpolateFeature()` for kriging interpolation of values
 
+## Changes
+* GiottoVisuals (>= 0.2.0) and GiottoClass (>= 0.3.0) are now required.
+
 
 
 # Giotto 4.0.5 (2024/03/12)