Merge branch 'suite_dev' of https://github.com/drieslab/Giotto into s…

…uite_dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.9
+Version: 4.1.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -31,7 +31,7 @@ Depends:
     utils (>= 4.1.0),
     R (>= 4.1.0),
     methods,
-    GiottoClass (>= 0.3.1)
+    GiottoClass (>= 0.3.2)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -40,9 +40,8 @@ Imports:
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
-    ggrepel,
     GiottoUtils (>= 0.1.9),
-    GiottoVisuals (>= 0.2.2),
+    GiottoVisuals (>= 0.2.4),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
@@ -126,11 +125,18 @@ Suggests:
     trendsceek,
     testthat (>= 3.0.0),
     qs
+Remotes:
+    drieslab/GiottoUtils,
+    drieslab/GiottoClass,
+    drieslab/GiottoVisuals
 Collate:
     'auxiliary_giotto.R'
     'cell_segmentation.R'
     'clustering.R'
-    'convenience.R'
+    'convenience_cosmx.R'
+    'convenience_general.R'
+    'convenience_visiumHD.R'
+    'convenience_xenium.R'
     'cross_section.R'
     'dd.R'
     'differential_expression.R'

NAMESPACE

@@ -1,7 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,combIcfObject)
-S3method(print,icfObject)
+S3method(.DollarNames,CosmxReader)
+S3method(.DollarNames,VisiumHDReader)
+S3method(.DollarNames,XeniumReader)
 export("%>%")
 export("activeFeatType<-")
 export("activeSpatUnit<-")
@@ -151,6 +152,7 @@ export(crossSectionFeatPlot)
 export(crossSectionFeatPlot3D)
 export(crossSectionPlot)
 export(crossSectionPlot3D)
+export(density)
 export(detectSpatialCorFeats)
 export(detectSpatialCorFeatsMatrix)
 export(detectSpatialPatterns)
@@ -257,7 +259,10 @@ export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
 export(heatmSpatialCorGenes)
 export(hexVertices)
+export(hist)
 export(hyperGeometricEnrich)
+export(importCosMx)
+export(importVisiumHD)
 export(initHMRF_V2)
 export(insertCrossSectionFeatPlot3D)
 export(insertCrossSectionSpatPlot3D)
@@ -316,10 +321,13 @@ export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
 export(polyStamp)
+export(print.combIcfObject)
+export(print.icfObject)
 export(processGiotto)
 export(prov)
 export(rankEnrich)
 export(rankSpatialCorGroups)
+export(read10xAffineImage)
 export(readCellMetadata)
 export(readDimReducData)
 export(readExprData)
@@ -488,6 +496,8 @@ export(violinPlot)
 export(wrap)
 export(writeGiottoLargeImage)
 export(writeHMRFresults)
+exportMethods("$")
+exportMethods("$<-")
 exportMethods(interpolateFeature)
 import(GiottoClass)
 import(GiottoUtils)
@@ -586,6 +596,7 @@ importFrom(GiottoClass,createSpatialNetwork)
 importFrom(GiottoClass,createSpatialWeightMatrix)
 importFrom(GiottoClass,crop)
 importFrom(GiottoClass,cropGiottoLargeImage)
+importFrom(GiottoClass,density)
 importFrom(GiottoClass,distGiottoImage)
 importFrom(GiottoClass,estimateImageBg)
 importFrom(GiottoClass,ext)
@@ -620,6 +631,7 @@ importFrom(GiottoClass,giottoToSeuratV4)
 importFrom(GiottoClass,giottoToSeuratV5)
 importFrom(GiottoClass,giottoToSpatialExperiment)
 importFrom(GiottoClass,hexVertices)
+importFrom(GiottoClass,hist)
 importFrom(GiottoClass,installGiottoEnvironment)
 importFrom(GiottoClass,instructions)
 importFrom(GiottoClass,joinGiottoObjects)

NEWS.md

@@ -4,6 +4,9 @@
 * 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.
 
+## New
+* `read10xAffineImage()` for reading 10x affine tranformed images
+
 # Giotto 4.0.9
 
 ## Breaking changes

R/auxiliary_giotto.R

@@ -437,7 +437,7 @@ filterCombinations <- function(
     pl <- pl + scale_color_discrete(
         guide = guide_legend(title = "threshold(s)")
     )
-    pl <- pl + ggrepel::geom_text_repel(data = result_DT, aes(
+    pl <- pl + geom_text_repel(data = result_DT, aes(
         x = removed_cells + x_axis_offset,
         y = removed_feats + y_axis_offset,
         label = combination