Merge pull request #1003 from drieslab/suite_dev

v4.1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.8
+Version: 4.1.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -25,13 +25,13 @@ Encoding: UTF-8
 LazyData: true
 URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends:
     base (>= 4.1.0),
     utils (>= 4.1.0),
     R (>= 4.1.0),
     methods,
-    GiottoClass (>= 0.3.1)
+    GiottoClass (>= 0.3.3)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -40,9 +40,8 @@ Imports:
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
-    ggrepel,
-    GiottoUtils (>= 0.1.8),
-    GiottoVisuals (>= 0.2.2),
+    GiottoUtils (>= 0.1.9),
+    GiottoVisuals (>= 0.2.4),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
@@ -61,7 +60,6 @@ Imports:
 Suggests:
     ArchR,
     arrow,
-    Biobase,
     biomaRt,
     ClusterR,
     clustree,
@@ -70,14 +68,12 @@ Suggests:
     DelayedMatrixStats,
     dendextend (>= 1.13.0),
     dplyr,
-    exactextractr,
     FactoMineR,
     factoextra,
     fitdistrplus,
     FNN,
     future,
     future.apply,
-    geometry,
     GiottoData,
     ggalluvial,
     ggdendro,
@@ -87,7 +83,6 @@ Suggests:
     graphcoloring,
     HDF5Array (>= 1.18.1),
     hdf5r,
-    htmlwidgets,
     jackstraw,
     kableExtra,
     knitr,
@@ -96,7 +91,6 @@ Suggests:
     multinet (>= 3.0.2),
     networkD3,
     pheatmap,
-    png,
     quadprog,
     harmony,
     R.utils,
@@ -106,10 +100,7 @@ Suggests:
     rhdf5,
     RTriangle (>= 1.6-0.10),
     Rvision,
-    S4Vectors,
     scater,
-    scatterpie,
-    scattermore,
     scran (>= 1.10.1),
     Seurat,
     sf,
@@ -122,19 +113,22 @@ Suggests:
     STexampleData,
     SummarizedExperiment,
     tidygraph,
-    tiff,
     trendsceek,
     testthat (>= 3.0.0),
-    qs
+    rmarkdown
 Remotes:
     drieslab/GiottoUtils,
     drieslab/GiottoClass,
     drieslab/GiottoVisuals
 Collate:
+    'ONTraC_wrapper.R'
     '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

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,CosmxReader)
+S3method(.DollarNames,VisiumHDReader)
+S3method(.DollarNames,XeniumReader)
 export("%>%")
 export("activeFeatType<-")
 export("activeSpatUnit<-")
@@ -55,6 +58,7 @@ export(binSpect)
 export(binSpectMulti)
 export(binSpectSingle)
 export(binSpectSingleMatrix)
+export(calculateAffineMatrixFromLandmarks)
 export(calculateHVF)
 export(calculateMetaTable)
 export(calculateMetaTableCells)
@@ -149,9 +153,9 @@ export(crossSectionFeatPlot)
 export(crossSectionFeatPlot3D)
 export(crossSectionPlot)
 export(crossSectionPlot3D)
+export(density)
 export(detectSpatialCorFeats)
 export(detectSpatialCorFeatsMatrix)
-export(detectSpatialCorGenes)
 export(detectSpatialPatterns)
 export(dimCellPlot)
 export(dimCellPlot2D)
@@ -163,6 +167,7 @@ export(dimPlot2D)
 export(dimPlot3D)
 export(distGiottoImage)
 export(doCellSegmentation)
+export(doCellposeSegmentation)
 export(doClusterProjection)
 export(doFeatureSetEnrichment)
 export(doGiottoClustree)
@@ -178,6 +183,7 @@ export(doLouvainSubCluster)
 export(doRandomWalkCluster)
 export(doSNNCluster)
 export(doScrubletDetect)
+export(estimateAutomatedImageRegistrationWithSIFT)
 export(estimateImageBg)
 export(exportGiottoViewer)
 export(exprCellCellcom)
@@ -235,6 +241,8 @@ export(getGEFtxCoords)
 export(getGiottoImage)
 export(getMultiomics)
 export(getNearestNetwork)
+export(getONTraCv1Input)
+export(getONTraCv2Input)
 export(getPolygonInfo)
 export(getRainbowColors)
 export(getSpatialEnrichment)
@@ -256,16 +264,23 @@ export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
 export(heatmSpatialCorGenes)
 export(hexVertices)
+export(hist)
 export(hyperGeometricEnrich)
+export(identifyTMAcores)
+export(importCosMx)
+export(importVisiumHD)
+export(importXenium)
 export(initHMRF_V2)
 export(insertCrossSectionFeatPlot3D)
 export(insertCrossSectionSpatPlot3D)
 export(installGiottoEnvironment)
 export(instructions)
+export(interactiveLandmarkSelection)
 export(jackstrawPlot)
 export(joinGiottoObjects)
 export(loadGiotto)
 export(loadHMRF)
+export(loadOntraCResults)
 export(makePseudoVisium)
 export(makeSignMatrixDWLS)
 export(makeSignMatrixDWLSfromMatrix)
@@ -285,8 +300,11 @@ export(pieCellTypesFromEnrichment)
 export(plotCCcomDotplot)
 export(plotCCcomHeatmap)
 export(plotCPF)
+export(plotCTCompositionInNicheCluster)
+export(plotCTCompositionInProbCluster)
 export(plotCellProximityFeatSpot)
 export(plotCellProximityFeats)
+export(plotCellTypeNTScore)
 export(plotCellTypesFromEnrichment)
 export(plotCombineCCcom)
 export(plotCombineCellCellCommunication)
@@ -301,6 +319,7 @@ export(plotInteractive3D)
 export(plotInteractivePolygons)
 export(plotMetaDataCellsHeatmap)
 export(plotMetaDataHeatmap)
+export(plotNicheClusterConnectivity)
 export(plotPCA)
 export(plotPCA_2D)
 export(plotPCA_3D)
@@ -315,10 +334,14 @@ export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
 export(polyStamp)
+export(preprocessImageToMatrix)
+export(print.combIcfObject)
+export(print.icfObject)
 export(processGiotto)
 export(prov)
 export(rankEnrich)
 export(rankSpatialCorGroups)
+export(read10xAffineImage)
 export(readCellMetadata)
 export(readDimReducData)
 export(readExprData)
@@ -485,8 +508,11 @@ export(viewHMRFresults3D)
 export(viewHMRFresults_V2)
 export(violinPlot)
 export(wrap)
+export(writeChatGPTqueryDEG)
 export(writeGiottoLargeImage)
 export(writeHMRFresults)
+exportMethods("$")
+exportMethods("$<-")
 exportMethods(interpolateFeature)
 import(GiottoClass)
 import(GiottoUtils)
@@ -585,6 +611,7 @@ importFrom(GiottoClass,createSpatialNetwork)
 importFrom(GiottoClass,createSpatialWeightMatrix)
 importFrom(GiottoClass,crop)
 importFrom(GiottoClass,cropGiottoLargeImage)
+importFrom(GiottoClass,density)
 importFrom(GiottoClass,distGiottoImage)
 importFrom(GiottoClass,estimateImageBg)
 importFrom(GiottoClass,ext)
@@ -619,6 +646,7 @@ 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

@@ -1,3 +1,31 @@
+# Giotto 4.1.0 (2024/07/31)
+
+## Breaking changes
+* Deprecated `detectSpatialCorGenes()` removed. Use `detectSpatialCorFeats()` instead
+* Deprecated `findInteractionChangedGenes()` removed. Use `findInteractionChangedFeats()` instead
+* Deprecated `findCellProximityGenes()` removed. Use `findInteractionChangedFeats()` instead
+* `createGiottoXeniumObject()` has been overhauled and parameters have changed.
+
+## Bug fixes
+* 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.
+* Fix error in `interpolateFeatures()` where feature names with `-` or starting with numbers did not work
+* Add catch in `runPCAprojectionBatch()` for when ncp requested exceeds number of feats used
+* Make `spatCellCellcom()` respect `verbose` flag [#949](https://github.com/drieslab/Giotto/issues/949) by rbutleriii
+
+## New
+* Dataset affine registration via interactive shiny app and automated SIFT detection
+* Cell segmentation via Cellpose
+* `read10xAffineImage()` for reading 10x affine transformed images
+* Several modular importer and convenience functions
+* ONTraC implementation
+
+## Enhancements
+* `print()` methods for `icfObject` and `combIcfObject`
+
+## Changes
+* require GiottoUtils (>= 0.1.10)
+* require GiottoClass (>= 0.3.3)
 
 # Giotto 4.0.8 (2024/05/22)