Merge pull request #1081 from drieslab/suite

chore: catch up to suite

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.4
+Version: 4.1.6
 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 (>= 4.4.0),
     methods,
-    GiottoClass (>= 0.4.1)
+    GiottoClass (>= 0.4.5)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -37,8 +37,8 @@ Imports:
     dbscan (>= 1.1-3),
     ggraph,
     ggplot2 (>= 3.1.1),
-    GiottoUtils (>= 0.2.0),
-    GiottoVisuals (>= 0.2.6),
+    GiottoUtils (>= 0.2.2),
+    GiottoVisuals (>= 0.2.10),
     igraph (>= 1.2.4.1),
     Matrix (>= 1.6-2),
     MatrixGenerics,

NAMESPACE

@@ -177,9 +177,12 @@ export(doLeidenClusterIgraph)
 export(doLeidenSubCluster)
 export(doLouvainCluster)
 export(doLouvainSubCluster)
+export(doMesmerSegmentation)
 export(doRandomWalkCluster)
 export(doSNNCluster)
 export(doScrubletDetect)
+export(doStardistSegmentation)
+export(dotPlot)
 export(estimateAutomatedImageRegistrationWithSIFT)
 export(estimateImageBg)
 export(exportGiottoViewer)
@@ -751,6 +754,7 @@ importFrom(GiottoVisuals,dimGenePlot3D)
 importFrom(GiottoVisuals,dimPlot)
 importFrom(GiottoVisuals,dimPlot2D)
 importFrom(GiottoVisuals,dimPlot3D)
+importFrom(GiottoVisuals,dotPlot)
 importFrom(GiottoVisuals,getColors)
 importFrom(GiottoVisuals,giottoSankeyPlan)
 importFrom(GiottoVisuals,plotHeatmap)

NEWS.md

@@ -1,4 +1,44 @@
 
+# Giotto 4.1.6 (2024/12/09)
+
+## Bug fixes
+* `doScrubletDetect()` seed setting
+
+## Enhancements
+* `labelTransfer()` now has `integration_method = "harmony"` for label transferring with an integration pipeline. See ?labelTransfer and the `integration_method` section.
+* `importXenium()` `load_transcripts()` can now return a `data.table` rather than the `giottoPoints` representation
+
+## New
+* `doMesmerSegmentation()` and `doStardistSegmentation()` segmentation wrappers
+* `.varexp()` internal for calculating SVD variance determined with support for partial SVDs
+* `.cumvar()` internal for calculating cumulative variance explained
+* re-export of `dotPlot()` from GiottoVisuals
+
+## Changes
+* GiottoClass req raised to 0.4.5
+* GiottoUtils req raised to 0.2.2
+* GiottoVisuals req raised to 0.2.10
+
+
+# Giotto 4.1.5 (2024/11/08)
+
+## Enhancements
+* `createGiottoXeniumObject()` auto loading for morphology focus images, image directory loading, auto centroid calculation, allow skipping transcript loading
+
+## Website changes
+* New Analysis mini tutorials for showing common processing functions independently of the spatial technology.
+* New Slide-seq and OpenST examples.
+* New Contributing tab with guidelines for contributing to the package and the website.
+* New Visualizations tutorials.
+* New Giotto workflow and Core Functions tutorials under Get Started tab.
+* New Create and change Giotto instructions tutorial.
+* New Spatial Patterns tutorials section.
+* New tutorials under Interactivity for regions selection with vitessceR.
+* New Multi-samples tutorials section.
+* Updated technologies examples.
+* Updated tutorials for using Docker and Singularity Giotto containers.
+* Homogenized variable names across examples and tutorials.
+
 # Giotto 4.1.4 (2024/10/30)
 
 ## Changes