Merge pull request #645 from drieslab/suite_dev

3.3.0 update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 3.2
+Version: 3.3.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -33,15 +33,13 @@ Imports:
     cowplot (>= 0.9.4),
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
-    DelayedArray,
-    DelayedMatrixStats,
-    future,
+    deldir (>= 1.0.6),
     future.apply,
     ggplot2 (>= 3.1.1),
+    ggrepel,
     grDevices,
     graphics,
     igraph (>= 1.2.4.1),
-    irlba,
     jsonlite,
     limma,
     Matrix,
@@ -55,12 +53,11 @@ Imports:
     RColorBrewer (>= 1.1-2),
     reshape2,
     reticulate (>= 1.25),
-    rmarkdown,
-    R.utils,
     Rtsne (>= 0.15),
     scales (>= 1.0.0),
     sp,
     sparseMatrixStats,
+    stats,
     terra (>= 1.5-12),
     uwot (>= 0.0.0.9010)
 Suggests:
@@ -70,7 +67,8 @@ Suggests:
     circlize,
     ClusterR,
     ComplexHeatmap (>= 1.20.0),
-    deldir,
+    DelayedArray,
+    DelayedMatrixStats,
     dendextend (>= 1.13.0),
     dplyr,
     exactextractr,
@@ -87,6 +85,7 @@ Suggests:
     HDF5Array (>= 1.18.1),
     hdf5r,
     htmlwidgets,
+    irlba,
     jackstraw,
     knitr,
     MAST,
@@ -125,6 +124,9 @@ Collate:
     'clustering.R'
     'convenience.R'
     'cross_section.R'
+    'data_evaluation.R'
+    'data_input.R'
+    'dd.R'
     'differential_expression.R'
     'dimension_reduction.R'
     'general_help.R'

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(t,spatLocsObj)
+S3method(t,spatialNetworkObj)
 export("%>%")
 export(PAGEEnrich)
 export(addCellIntMetadata)
@@ -30,6 +32,7 @@ export(aggregateStacksExpression)
 export(aggregateStacksLocations)
 export(aggregateStacksPolygonOverlaps)
 export(aggregateStacksPolygons)
+export(aggregateStacksPolygonsOLD)
 export(anndataToGiotto)
 export(annotateGiotto)
 export(annotateSpatialGrid)
@@ -80,7 +83,10 @@ export(compareCellAbundance)
 export(comparePolygonExpression)
 export(convertEnsemblToGeneSymbol)
 export(convertGiottoLargeImageToMG)
+export(createCellMetaObj)
 export(createCrossSection)
+export(createDimObj)
+export(createFeatMetaObj)
 export(createGiottoCosMxObject)
 export(createGiottoImage)
 export(createGiottoImageOLD)
@@ -97,7 +103,11 @@ export(createGiottoVisiumObject)
 export(createGiottoXeniumObject)
 export(createMetafeats)
 export(createMetagenes)
+export(createNearestNetObj)
 export(createNearestNetwork)
+export(createSpatEnrObj)
+export(createSpatLocsObj)
+export(createSpatNetObj)
 export(createSpatialDefaultGrid)
 export(createSpatialDelaunayNetwork)
 export(createSpatialEnrich)
@@ -140,6 +150,7 @@ export(estimateImageBg)
 export(exportGiottoViewer)
 export(exprCellCellcom)
 export(fDataDT)
+export(featExpDWLS)
 export(featType)
 export(featureNetwork)
 export(fiji)
@@ -149,17 +160,17 @@ export(filterCombinations)
 export(filterDistributions)
 export(filterGiotto)
 export(filterICF)
+export(filterICFSpot)
 export(filterICG)
-export(filterICGSpot)
 export(filterInteractionChangedFeats)
 export(filterInteractionChangedGenes)
 export(findCPG)
 export(findCellProximityGenes)
 export(findGiniMarkers)
 export(findGiniMarkers_one_vs_all)
 export(findICF)
+export(findICFSpot)
 export(findICG)
-export(findICGSpot)
 export(findInteractionChangedFeats)
 export(findInteractionChangedGenes)
 export(findMarkers)
@@ -170,29 +181,30 @@ export(findNetworkNeighbors)
 export(findScranMarkers)
 export(findScranMarkers_one_vs_all)
 export(gefToGiotto)
-export(geneExpDWLS)
 export(get10Xmatrix)
 export(get10Xmatrix_h5)
 export(getBalancedSpatCoexpressionFeats)
+export(getCellMetadata)
 export(getCellsFromPolygon)
 export(getClusterSimilarity)
 export(getDendrogramSplits)
 export(getDimReduction)
 export(getDistinctColors)
 export(getExpression)
 export(getFeatureInfo)
+export(getFeatureMetadata)
 export(getGEFtxCoords)
 export(getGiottoImage)
 export(getMultiomics)
 export(getNearestNetwork)
 export(getPolygonInfo)
+export(getRainbowColors)
 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)
@@ -236,9 +248,9 @@ export(plotCCcomDotplot)
 export(plotCCcomHeatmap)
 export(plotCPF)
 export(plotCPG)
+export(plotCellProximityFeatSpot)
 export(plotCellProximityFeats)
 export(plotCellProximityGenes)
-export(plotCellProximityGenesSpot)
 export(plotCombineCCcom)
 export(plotCombineCPG)
 export(plotCombineCellCellCommunication)
@@ -249,8 +261,8 @@ export(plotCombineInteractionChangedGenes)
 export(plotGiottoImage)
 export(plotHeatmap)
 export(plotICF)
+export(plotICFSpot)
 export(plotICG)
-export(plotICGSpot)
 export(plotInteractionChangedFeats)
 export(plotInteractionChangedGenes)
 export(plotInteractivePolygons)
@@ -269,17 +281,26 @@ export(plotTSNE_3D)
 export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
-export(plot_spat_voronoi_layer_ggplot)
 export(polyStamp)
 export(processGiotto)
 export(prov)
 export(rankEnrich)
 export(rankSpatialCorGroups)
+export(readCellMetadata)
+export(readDimReducData)
+export(readExprData)
 export(readExprMatrix)
+export(readFeatData)
+export(readFeatMetadata)
 export(readGiottoInstructions)
+export(readNearestNetData)
+export(readPolygonData)
 export(readPolygonFilesVizgen)
 export(readPolygonFilesVizgenHDF5)
 export(readPolygonFilesVizgenHDF5_old)
+export(readSpatEnrichData)
+export(readSpatLocsData)
+export(readSpatNetData)
 export(reconnectGiottoImage)
 export(rectVertices)
 export(registerGiottoObjectList)
@@ -290,6 +311,7 @@ export(removeCellAnnotation)
 export(removeFeatAnnotation)
 export(removeGiottoEnvironment)
 export(replaceGiottoInstructions)
+export(rescalePolygons)
 export(runDWLSDeconv)
 export(runGiottoHarmony)
 export(runHyperGeometricEnrich)
@@ -406,13 +428,14 @@ export(subClusterCells)
 export(subsetGiotto)
 export(subsetGiottoLocs)
 export(subsetGiottoLocsMulti)
-export(t.spatLocsObj)
-export(t.spatialNetworkObj)
+export(subsetGiottoLocsSubcellular)
 export(trendSceek)
 export(updateGiottoImage)
 export(updateGiottoImageMG)
 export(updateGiottoLargeImage)
 export(updateGiottoObject)
+export(updateGiottoPointsObject)
+export(updateGiottoPolygonObject)
 export(validObject)
 export(viewHMRFresults)
 export(viewHMRFresults2D)
@@ -440,18 +463,26 @@ exportMethods("$")
 exportMethods("$<-")
 exportMethods("[")
 exportMethods("[<-")
+exportMethods("activeFeatType<-")
+exportMethods("activeSpatUnit<-")
 exportMethods("featType<-")
+exportMethods("instructions<-")
 exportMethods("objName<-")
 exportMethods("prov<-")
 exportMethods("spatUnit<-")
+exportMethods(activeFeatType)
+exportMethods(activeSpatUnit)
+exportMethods(centroids)
 exportMethods(colnames)
 exportMethods(copy)
 exportMethods(dim)
 exportMethods(featIDs)
 exportMethods(featType)
+exportMethods(instructions)
 exportMethods(ncol)
 exportMethods(nrow)
 exportMethods(objName)
+exportMethods(overlaps)
 exportMethods(plot)
 exportMethods(prov)
 exportMethods(rbind2)
@@ -467,16 +498,20 @@ import(data.table)
 import(ggplot2)
 import(magrittr)
 import(utils)
+importFrom(graphics,segments)
 importFrom(magrittr,"%>%")
 importFrom(methods,"slot<-")
 importFrom(methods,new)
 importFrom(methods,rbind2)
 importFrom(methods,show)
 importFrom(methods,slot)
+importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importMethodsFrom(Matrix,t)
+importMethodsFrom(terra,centroids)
 importMethodsFrom(terra,ncol)
 importMethodsFrom(terra,nrow)
+importMethodsFrom(terra,plot)
 importMethodsFrom(terra,spin)
 importMethodsFrom(terra,t)
 importMethodsFrom(terra,vect)

NEWS.md

@@ -1,3 +1,61 @@
+
+
+
+# Giotto Suite 3.3.0 (2023-04-18)
+
+## Breaking Changes
+- Set Suite as default branch
+- Removed all deprecated accessors from `accessors.R`
+- `set_default_feat_type()` error downgraded to warning when no `feat_type`s exist for given `spat_unit`
+- update `loadGiotto()` and `saveGiotto()` to allow using long strings as column names in the spatVector objects
+- `'active_spat_unit'` and `'active_feat_type'` params that can be set through `instructions()` are now used instead of 'giotto.spat_unit' and 'giotto.feat_type' global options
+- removed duplicate `create_dimObject()` internal function. Keeping `create_dim_obj()`
+
+
+
+## Added
+- New implementations of `anndataToGiotto()` and `giottoToAnnData()` for Nearest Neighbor and Spatial Networks
+- New `check_py_for_scanpy()` function, shifting code around in `anndataToGiotto()`
+- Add `initialize()` method for `giotto`
+- Add exported `create` constructor functions for Giotto S4 subobjects
+- Add `activeSpatUnit()` and `activeFeatType()` for getting and setting active defaults on gobject
+- New `get_*_list()` internal functions for retrieving list of all objects of a particular class for a spat_unit and feat_type
+- Add `instructions()` generic for `giotto` to access and edit `giottoInstructions`
+- Add `centroids()` method for `giottoPolygon` to get centroid info
+- Add `overlaps()` generic for accessing `overlaps` slot of `giottoPolygon`
+- Add `[` and `[<-` (empty) access generics to get the data from main slots of `giottoPolygon` and `giottoPoints`
+- Add cores detection to run on package attach. (`getOption('giotto.cores')`)
+- Add option to return as `giottoPoints` from `getFeatureInfo` (default is still `SpatVector`)
+- Add `spatVector_to_dt2` internal as a barebones alternative to `spatVector_to_dt()`
+- Add `getRainbowColors()` color palette
+- New `assign_objnames_2_list()` and `assign_listnames_2_obj()` internals for passing list names to object `@name` slots and vice versa
+- New test_that `test_createObject.R` script for `read` functions/S4 subobject creation
+- New test_that `test_accessors.R` script for `accessor` functions
+- New test_that `test_gobject.R` script for gobject consistency checks
+
+
+
+## Changes
+- Update `installGiottoEnvironment()` and downstream internal functions to allow custom python installation with a new argument, `mini_install_path`.
+- Update `checkGiottoEnvironment()` to account for custom python installations with a new argument, `mini_install_path`.
+- Update `removeGiottoEnvironment()` to account for custom python installations with a new argument, `mini_path`.
+- Update `createGiottoObject()` with new data ingestion pipeline
+- Modify `cell_ID`, `feat_ID`, `cell_metadata`, `feat_metadata` slot initialization
+- Update `read_expression_data()` and `evaluate_expr_matrix()` to be compatible with `exprObj`
+- Change `changeGiottoInstructions()` to allow addition of new params and enforce logical class of known params
+- Update and fix bugs in `createGiottoCosMxObject()` associated with polygon placement and generation
+- Update `plot()` for `giottoPoints` with faster rasterized plotting option. (Now used by default)
+- Fix bug in `doLouvainCluster()` (sub)functions and made them compatible with new Giotto Suite framework.
+- Fix bug in `gefToGiotto()` bin_size arguments.
+- Update `loadGiotto()` and `saveGiotto()` with path.expand to expand provided file/directory paths
+- Organize new and refactored slot `check` functions in `giotto.R` for checking gobject consistency during `initialize()`
+- Organize new and refactored `evaluate` functions in `data_evaluation.R` for data wrangling of external data
+- Organize new and refactored `read` functions in `data_input.R` for ingesting data and converting to list of Giotto native S4 subobjects
+- Organize dummy documentation in `dd.R` for inheriting commonly used documentation
+- Moved `create_featureNetwork_object()`, `create_giotto_points_object()`, `create_giotto_polygon_object()` to classes.R
+- Moved `depth()` from giotto.R to utilities.R
+
+
 # Giotto Suite 3.2.0 (2023-02-02)
 
 ## Breaking Changes