Merge pull request #534 from jiajic/suite

3.2.0 update

.github/workflows/R-CMD-check.yaml

@@ -3,11 +3,13 @@
 on:
   push:
     branches:
-      - 'ci-unittest' 
+      - 'ci-unittest'
       - 'suite' # run workflow on push to branch
+      - 'suite_dev'
   pull_request:
     branches:
       - 'suite'
+      - 'suite_dev'
 
 name: R-CMD-check
 
@@ -36,17 +38,17 @@ jobs:
       - name: Remove vignettes dir
         run: rm -rf 'vignettes/'
         shell: bash
-      
+
       # checkout repo for workflow access
-      - uses: actions/checkout@v2 
+      - uses: actions/checkout@v2
 
       # setup R
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-      
+
       # setup dependencies
       - uses: r-lib/actions/setup-r-dependencies@v2
         env:
@@ -61,7 +63,7 @@ jobs:
         with:
           upload-snapshots: true
           error-on: '"error"' # workflow errors on error only, can change to include warnings
-      
+
       # show testthat output for ease of access
       - name: Show testthat output
         if: always()

.gitignore

@@ -6,4 +6,6 @@ inst/doc
 *.Rproj
 .git_old
 merfish_preoptic/
-.vscode/launch.json
+.vscode/*
+.Rprofile
+inst/python/.ipynb_checkpoints/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 3.1
+Version: 3.2
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -11,6 +11,8 @@ Authors@R: c(
 	person("Guo-Cheng", "Yuan", email = "[email protected]",
 		 role = c("aut")),
     person("Matthew", "O'Brien", email = "[email protected]",
+		 role = c("aut")),
+		 person("Joselyn", "Chávez", email = "[email protected]",
 		 role = c("aut"))
 	)
 Maintainer: Ruben Dries <[email protected]>
@@ -20,7 +22,7 @@ Encoding: UTF-8
 LazyData: true
 URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Depends:
     base (>= 3.5.0),
     utils (>= 3.5.0),
@@ -49,6 +51,7 @@ Imports:
     matrixStats (>= 0.55.0),
     plotly,
     parallel,
+    progressr,
     RColorBrewer (>= 1.1-2),
     reshape2,
     reticulate (>= 1.25),
@@ -70,6 +73,7 @@ Suggests:
     deldir,
     dendextend (>= 1.13.0),
     dplyr,
+    exactextractr,
     FactoMineR,
     factoextra,
     fitdistrplus,
@@ -97,6 +101,7 @@ Suggests:
     Rvision,
     S4Vectors,
     Seurat,
+    sf,
     scatterpie,
     scattermore,
     scran (>= 1.10.1),
@@ -118,13 +123,14 @@ Collate:
     'cell_segmentation.R'
     'classes.R'
     'clustering.R'
+    'convenience.R'
     'cross_section.R'
     'differential_expression.R'
     'dimension_reduction.R'
     'general_help.R'
+    'giotto_structures.R'
     'generics.R'
     'giotto.R'
-    'giotto_structures.R'
     'giotto_viewer.R'
     'globals.R'
     'image_registration.R'
@@ -138,13 +144,15 @@ Collate:
     'spatial_genes.R'
     'spatial_in_situ_visuals.R'
     'spatial_interaction.R'
+    'spatial_interaction_spot.R'
     'spatial_interaction_visuals.R'
     'spatial_structures.R'
     'spatial_visuals.R'
     'utilities.R'
     'utils-pipe.R'
     'variable_genes.R'
     'wnn.R'
+    'zzz.R'
 biocViews:
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -48,6 +48,8 @@ export(calculateOverlapRaster)
 export(calculateOverlapSerial)
 export(cellProximityBarplot)
 export(cellProximityEnrichment)
+export(cellProximityEnrichmentEachSpot)
+export(cellProximityEnrichmentSpots)
 export(cellProximityHeatmap)
 export(cellProximityNetwork)
 export(cellProximitySpatPlot)
@@ -85,6 +87,7 @@ export(createGiottoImageOLD)
 export(createGiottoInstructions)
 export(createGiottoLargeImage)
 export(createGiottoLargeImageList)
+export(createGiottoMerscopeObject)
 export(createGiottoObject)
 export(createGiottoObjectSubcellular)
 export(createGiottoPoints)
@@ -102,6 +105,7 @@ export(createSpatialFeaturesKNNnetwork)
 export(createSpatialGrid)
 export(createSpatialKNNnetwork)
 export(createSpatialNetwork)
+export(createSpatialWeightMatrix)
 export(cropGiottoLargeImage)
 export(crossSectionGenePlot)
 export(crossSectionGenePlot3D)
@@ -146,6 +150,7 @@ export(filterDistributions)
 export(filterGiotto)
 export(filterICF)
 export(filterICG)
+export(filterICGSpot)
 export(filterInteractionChangedFeats)
 export(filterInteractionChangedGenes)
 export(findCPG)
@@ -154,6 +159,7 @@ export(findGiniMarkers)
 export(findGiniMarkers_one_vs_all)
 export(findICF)
 export(findICG)
+export(findICGSpot)
 export(findInteractionChangedFeats)
 export(findInteractionChangedGenes)
 export(findMarkers)
@@ -163,19 +169,33 @@ export(findMastMarkers_one_vs_all)
 export(findNetworkNeighbors)
 export(findScranMarkers)
 export(findScranMarkers_one_vs_all)
+export(gefToGiotto)
+export(geneExpDWLS)
 export(get10Xmatrix)
 export(get10Xmatrix_h5)
 export(getBalancedSpatCoexpressionFeats)
 export(getCellsFromPolygon)
 export(getClusterSimilarity)
 export(getDendrogramSplits)
+export(getDimReduction)
 export(getDistinctColors)
+export(getExpression)
+export(getFeatureInfo)
 export(getGEFtxCoords)
+export(getGiottoImage)
+export(getMultiomics)
+export(getNearestNetwork)
+export(getPolygonInfo)
+export(getSpatialEnrichment)
+export(getSpatialGrid)
+export(getSpatialLocations)
+export(getSpatialNetwork)
 export(get_NearestNetwork)
 export(get_dimReduction)
 export(get_expression_values)
 export(get_feature_info)
 export(get_giottoImage)
+export(get_multiomics)
 export(get_polygon_info)
 export(get_spatialGrid)
 export(get_spatialNetwork)
@@ -186,6 +206,7 @@ export(giottoImage)
 export(giottoLargeImage)
 export(giottoPoints)
 export(giottoPolygon)
+export(giottoToAnnData)
 export(giottoToSeurat)
 export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
@@ -206,6 +227,7 @@ export(makeSignMatrixRank)
 export(mergeClusters)
 export(normalizeGiotto)
 export(objHistory)
+export(objName)
 export(overlapImagesToMatrix)
 export(overlapToMatrix)
 export(overlapToMatrixMultiPoly)
@@ -216,6 +238,7 @@ export(plotCPF)
 export(plotCPG)
 export(plotCellProximityFeats)
 export(plotCellProximityGenes)
+export(plotCellProximityGenesSpot)
 export(plotCombineCCcom)
 export(plotCombineCPG)
 export(plotCombineCellCellCommunication)
@@ -227,6 +250,7 @@ export(plotGiottoImage)
 export(plotHeatmap)
 export(plotICF)
 export(plotICG)
+export(plotICGSpot)
 export(plotInteractionChangedFeats)
 export(plotInteractionChangedGenes)
 export(plotInteractivePolygons)
@@ -255,6 +279,7 @@ export(readExprMatrix)
 export(readGiottoInstructions)
 export(readPolygonFilesVizgen)
 export(readPolygonFilesVizgenHDF5)
+export(readPolygonFilesVizgenHDF5_old)
 export(reconnectGiottoImage)
 export(rectVertices)
 export(registerGiottoObjectList)
@@ -282,11 +307,23 @@ export(runtSNE)
 export(saveGiotto)
 export(screePlot)
 export(selectPatternGenes)
+export(setDimReduction)
+export(setExpression)
+export(setFeatureInfo)
+export(setGiottoImage)
+export(setMultiomics)
+export(setNearestNetwork)
+export(setPolygonInfo)
+export(setSpatialEnrichment)
+export(setSpatialGrid)
+export(setSpatialLocations)
+export(setSpatialNetwork)
 export(set_NearestNetwork)
 export(set_dimReduction)
 export(set_expression_values)
 export(set_feature_info)
 export(set_giottoImage)
+export(set_multiomics)
 export(set_polygon_info)
 export(set_spatialGrid)
 export(set_spatialNetwork)
@@ -327,6 +364,7 @@ export(slot)
 export(smoothGiottoPolygons)
 export(spark)
 export(spatCellCellcom)
+export(spatCellCellcomSpots)
 export(spatCellPlot)
 export(spatCellPlot2D)
 export(spatDeconvPlot)
@@ -353,9 +391,13 @@ export(spatNetwDistributionsKneighbors)
 export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
+export(spatShift)
 export(spatUnit)
 export(spatialAEH)
+export(spatialAutoCorGlobal)
+export(spatialAutoCorLocal)
 export(spatialDE)
+export(spatialExperimentToGiotto)
 export(specificCellCellcommunicationScores)
 export(stitchFieldCoordinates)
 export(stitchGiottoLargeImage)
@@ -364,6 +406,8 @@ export(subClusterCells)
 export(subsetGiotto)
 export(subsetGiottoLocs)
 export(subsetGiottoLocsMulti)
+export(t.spatLocsObj)
+export(t.spatialNetworkObj)
 export(trendSceek)
 export(updateGiottoImage)
 export(updateGiottoImageMG)
@@ -386,6 +430,7 @@ exportClasses(giottoImage)
 exportClasses(giottoLargeImage)
 exportClasses(giottoPoints)
 exportClasses(giottoPolygon)
+exportClasses(nnNetObj)
 exportClasses(spatEnrObj)
 exportClasses(spatLocsObj)
 exportClasses(spatialGridObj)
@@ -395,23 +440,43 @@ exportMethods("$<-")
 exportMethods("[")
 exportMethods("[<-")
 exportMethods("featType<-")
+exportMethods("objName<-")
 exportMethods("prov<-")
 exportMethods("spatUnit<-")
+exportMethods(colnames)
 exportMethods(copy)
 exportMethods(dim)
+exportMethods(featIDs)
 exportMethods(featType)
 exportMethods(ncol)
 exportMethods(nrow)
+exportMethods(objName)
 exportMethods(plot)
 exportMethods(prov)
+exportMethods(rbind2)
+exportMethods(rownames)
+exportMethods(spatIDs)
+exportMethods(spatShift)
 exportMethods(spatUnit)
+exportMethods(spin)
+exportMethods(t)
+exportMethods(vect)
+exportMethods(wrap)
 import(data.table)
 import(ggplot2)
 import(magrittr)
 import(utils)
 importFrom(magrittr,"%>%")
 importFrom(methods,"slot<-")
 importFrom(methods,new)
+importFrom(methods,rbind2)
 importFrom(methods,show)
 importFrom(methods,slot)
 importFrom(methods,validObject)
+importMethodsFrom(Matrix,t)
+importMethodsFrom(terra,ncol)
+importMethodsFrom(terra,nrow)
+importMethodsFrom(terra,spin)
+importMethodsFrom(terra,t)
+importMethodsFrom(terra,vect)
+importMethodsFrom(terra,wrap)