Merge pull request #1103 from jiajic/cosmx_patch

hotfix: cosmx convenience

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.2.2
+Version: 4.2.1
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -28,7 +28,7 @@ RoxygenNote: 7.3.2
 Depends:
     R (>= 4.4.1),
     methods,
-    GiottoClass (>= 0.4.5)
+    GiottoClass (>= 0.4.7)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -38,7 +38,7 @@ Imports:
     ggraph,
     ggplot2 (>= 3.1.1),
     GiottoUtils (>= 0.2.4),
-    GiottoVisuals (>= 0.2.10),
+    GiottoVisuals (>= 0.2.12),
     igraph (>= 1.2.4.1),
     Matrix (>= 1.6-2),
     MatrixGenerics,

NEWS.md

@@ -1,12 +1,18 @@
-# Giotto 4.2.2
+# Giotto 4.2.1 (2025/02/04)
 
 ## Changes
 * GiottoUtils req raised to 0.2.4
 
-# Giotto 4.2.1 (2025/02/04)
-
 ## Bug fixes
 * fix `identifyTMAcores()` when no overlap relations are found and an `rbind` error is thrown
+* fix `createGiottoCosMxObject()` not passing `load_expression`, `load_cellmeta`, `load_transcripts` params to `importCosMx()`
+
+## Enhancements
+* `poly_pref` param for `createGiottoCosMxObject()` and `importCosMx()` to select between loading the mask images or the `polygons.csv` as polygon info. 
+* `image_negative_y` param for `createGiottoCosMxObject()` for toggling how images and polygons from mask images should be spatially mapped
+* `slide` param made more prominent in `createGiottoCosMxObject()`
+* `importCosMx()` now supports vectors of filepaths when provided to `$load_images()` and `$load_polys()`
+* `importCosMx()` Selected FOVs are now selected in `plot()`.
 
 # Giotto 4.2.0 (2025/01/17)