feat: convHull()

DESCRIPTION

@@ -44,7 +44,7 @@ Imports:
     methods,
     reticulate (>= 1.25),
     stats,
-    terra (>= 1.7-39)
+    terra (>= 1.7-41)
 Suggests: 
     Biobase,
     chihaya,
@@ -109,6 +109,7 @@ Collate:
     'methods-affine.R'
     'methods-centroids.R'
     'methods-coerce.R'
+    'methods-convHull.R'
     'methods-copy.R'
     'methods-crop.R'
     'methods-dims.R'

NAMESPACE

@@ -320,6 +320,7 @@ exportMethods(as.terra)
 exportMethods(calculateOverlap)
 exportMethods(centroids)
 exportMethods(colnames)
+exportMethods(convHull)
 exportMethods(copy)
 exportMethods(createGiottoPoints)
 exportMethods(createGiottoPolygon)
@@ -335,6 +336,8 @@ exportMethods(flip)
 exportMethods(hist)
 exportMethods(instructions)
 exportMethods(intersect)
+exportMethods(minCircle)
+exportMethods(minRect)
 exportMethods(ncol)
 exportMethods(nrow)
 exportMethods(objName)
@@ -389,12 +392,15 @@ importMethodsFrom(terra,as.data.frame)
 importMethodsFrom(terra,as.points)
 importMethodsFrom(terra,as.polygons)
 importMethodsFrom(terra,centroids)
+importMethodsFrom(terra,convHull)
 importMethodsFrom(terra,crop)
 importMethodsFrom(terra,density)
 importMethodsFrom(terra,ext)
 importMethodsFrom(terra,flip)
 importMethodsFrom(terra,hist)
 importMethodsFrom(terra,intersect)
+importMethodsFrom(terra,minCircle)
+importMethodsFrom(terra,minRect)
 importMethodsFrom(terra,ncol)
 importMethodsFrom(terra,nrow)
 importMethodsFrom(terra,plot)

NEWS.md

@@ -3,6 +3,7 @@
 
 ## breaking changes
 - stop exporting deprecated internal accessors
+- terra requirement raised to 1.7.41 for `minCircle()`
 
 ## bug fixes
 - fix `dimnames()` for some subobjects
@@ -34,6 +35,7 @@
 - `splitGiotto()` for splitting a Giotto object into a list of Giotto objects based on a cell metadata column
 - `as.list()` method for `giotto` to dump the data as a list of subobjects
 - `XY()` and `XY<-()` for accessing and setting coordinate values of subobjects as `matrix`
+- terra `convHull()`, `minRect()`, `minCircle()` for Giotto spatial vector classes
 
 
 # GiottoClass 0.3.5 (2024/08/28)

R/methods-convHull.R

@@ -0,0 +1,73 @@
+# docs ----------------------------------------------------------- #
+#' @title Convex hull, minimal bounding rotated rectangle, and minimal bounding circle
+#' @name convHull
+#' @description Get the convex hull, the minimal bounding rotated rectangle, 
+#' or minimal bounding circle of a Giotto spatial object or terra SpatVector
+#' @param x any of giotto image, giottoPolygon, giottoPoints, spatLocsObj, SpatVector
+#' @param by character (variable name), to get a new geometry for groups of input geometries
+#' @param \dots additional parameters to pass
+#' @examples
+#' sl <- GiottoData::loadSubObjectMini("spatLocsObj")
+#' gpoints <- GiottoData::loadSubObjectMini("giottoPoints")
+#' 
+#' h <- convHull(sl)
+#' plot(h)
+#' 
+#' r <- minRect(sl)
+#' plot(r)
+#' 
+#' circ <- minCircle(gpoints, by = "feat_ID")
+#' plot(circ, border = rainbow(100))
+#' 
+#' @returns SpatVector
+NULL
+# ---------------------------------------------------------------- #
+
+#' @rdname convHull
+#' @usage
+#' ## S4 method for signatures 'spatLocsObj', 'giottoPolygon', 'giottoPoints'
+#' convHull(x, by = "")
+#' @export
+setMethod("convHull", signature("spatLocsObj"), function(x, by = "") {
+    convHull(x = as.points(x), by = by)
+})
+#' @rdname convHull
+#' @usage NULL
+#' @export
+setMethod("convHull", signature("giottoSpatial"), function(x, by = "") {
+    convHull(x[], by = by)
+})
+
+
+#' @rdname convHull
+#' @usage
+#' ## S4 method for signatures 'spatLocsObj', 'giottoPolygon', 'giottoPoints'
+#' minRect(x, by = "")
+#' @export
+setMethod("minRect", signature("spatLocsObj"), function(x, by = "") {
+    minRect(x = as.points(x), by = by)
+})
+#' @rdname convHull
+#' @usage NULL
+#' @export
+setMethod("minRect", signature("giottoSpatial"), function(x, by = "") {
+    minRect(x[], by = by)
+})
+
+
+#' @rdname convHull
+#' @usage
+#' ## S4 method for signatures 'spatLocsObj', 'giottoPolygon', 'giottoPoints'
+#' minCircle(x, by = "")
+#' @export
+setMethod("minCircle", signature("spatLocsObj"), function(x, by = "") {
+    minCircle(x = as.points(x), by = by)
+})
+#' @rdname convHull
+#' @usage NULL
+#' @export
+setMethod("minCircle", signature("giottoSpatial"), function(x, by = "") {
+    minCircle(x[], by = by)
+})
+
+

R/package_imports.R

@@ -15,7 +15,7 @@
 #' @importMethodsFrom terra rescale
 #' @importMethodsFrom Matrix t
 #' @importMethodsFrom terra t
-#' @importMethodsFrom terra ext ext<-
+#' @importMethodsFrom terra ext ext<- convHull minCircle minRect
 #' @importMethodsFrom terra plot
 #' @importMethodsFrom terra wrap
 #' @importMethodsFrom terra zoom