Merge pull request #730 from jiajic/suite

3.3.1 update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 3.3.0
+Version: 3.3.1
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -30,6 +30,7 @@ Depends:
     methods
 Imports:
     BiocSingular,
+    checkmate,
     cowplot (>= 0.9.4),
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
@@ -81,7 +82,6 @@ Suggests:
     ggdendro,
     ggforce,
     ggraph,
-    ggrepel,
     HDF5Array (>= 1.18.1),
     hdf5r,
     htmlwidgets,
@@ -117,10 +117,11 @@ Suggests:
 Collate:
     'NN_network.R'
     'accessors.R'
+    'classes.R'
+    'assert.R'
     'auxiliary_giotto.R'
     'auxiliary_visuals.R'
     'cell_segmentation.R'
-    'classes.R'
     'clustering.R'
     'convenience.R'
     'cross_section.R'
@@ -129,16 +130,19 @@ Collate:
     'dd.R'
     'differential_expression.R'
     'dimension_reduction.R'
+    'feature_set_enrichment.R'
     'general_help.R'
     'giotto_structures.R'
     'generics.R'
     'giotto.R'
     'giotto_viewer.R'
     'globals.R'
+    'spatial_manipulation.R'
     'image_registration.R'
     'images.R'
     'interactivity.R'
     'interoperability.R'
+    'poly_influence.R'
     'python_environment.R'
     'python_hmrf.R'
     'python_scrublet.R'

NAMESPACE

@@ -21,6 +21,7 @@ export(addGiottoPoints)
 export(addGiottoPoints3D)
 export(addGiottoPolygons)
 export(addHMRF)
+export(addHMRF_V2)
 export(addNetworkLayout)
 export(addPolygonCells)
 export(addSpatialCentroidLocations)
@@ -83,9 +84,11 @@ export(compareCellAbundance)
 export(comparePolygonExpression)
 export(convertEnsemblToGeneSymbol)
 export(convertGiottoLargeImageToMG)
+export(createArchRProj)
 export(createCellMetaObj)
 export(createCrossSection)
 export(createDimObj)
+export(createExprObj)
 export(createFeatMetaObj)
 export(createGiottoCosMxObject)
 export(createGiottoImage)
@@ -96,6 +99,7 @@ export(createGiottoLargeImageList)
 export(createGiottoMerscopeObject)
 export(createGiottoObject)
 export(createGiottoObjectSubcellular)
+export(createGiottoObjectfromArchR)
 export(createGiottoPoints)
 export(createGiottoPolygonsFromDfr)
 export(createGiottoPolygonsFromMask)
@@ -112,6 +116,7 @@ export(createSpatialDefaultGrid)
 export(createSpatialDelaunayNetwork)
 export(createSpatialEnrich)
 export(createSpatialFeaturesKNNnetwork)
+export(createSpatialGenomicsObject)
 export(createSpatialGrid)
 export(createSpatialKNNnetwork)
 export(createSpatialNetwork)
@@ -136,7 +141,10 @@ export(dimPlot2D)
 export(dimPlot3D)
 export(distGiottoImage)
 export(doCellSegmentation)
+export(doFeatureSetEnrichment)
+export(doGiottoClustree)
 export(doHMRF)
+export(doHMRF_V2)
 export(doHclust)
 export(doKmeans)
 export(doLeidenCluster)
@@ -164,6 +172,7 @@ export(filterICFSpot)
 export(filterICG)
 export(filterInteractionChangedFeats)
 export(filterInteractionChangedGenes)
+export(filterSpatialGenes)
 export(findCPG)
 export(findCellProximityGenes)
 export(findGiniMarkers)
@@ -216,6 +225,7 @@ export(get_spatial_locations)
 export(giotto)
 export(giottoImage)
 export(giottoLargeImage)
+export(giottoMasterToSuite)
 export(giottoPoints)
 export(giottoPolygon)
 export(giottoToAnnData)
@@ -225,13 +235,15 @@ export(heatmSpatialCorFeats)
 export(heatmSpatialCorGenes)
 export(hexVertices)
 export(hyperGeometricEnrich)
+export(initHMRF_V2)
 export(insertCrossSectionGenePlot3D)
 export(insertCrossSectionSpatPlot3D)
 export(installGiottoEnvironment)
 export(jackstrawPlot)
 export(joinGiottoObjects)
 export(loadGiotto)
 export(loadHMRF)
+export(makePseudoVisium)
 export(makeSignMatrixDWLS)
 export(makeSignMatrixDWLSfromMatrix)
 export(makeSignMatrixPAGE)
@@ -298,6 +310,7 @@ export(readPolygonData)
 export(readPolygonFilesVizgen)
 export(readPolygonFilesVizgenHDF5)
 export(readPolygonFilesVizgenHDF5_old)
+export(readPolygonVizgenParquet)
 export(readSpatEnrichData)
 export(readSpatLocsData)
 export(readSpatNetData)
@@ -353,6 +366,8 @@ export(set_spatial_enrichment)
 export(set_spatial_locations)
 export(seuratToGiotto)
 export(seuratToGiotto_OLD)
+export(showCellProportionSwitchedPie)
+export(showCellProportionSwitchedSanKey)
 export(showClusterDendrogram)
 export(showClusterHeatmap)
 export(showGiottoCellMetadata)
@@ -374,6 +389,7 @@ export(showPattern)
 export(showPattern2D)
 export(showPattern3D)
 export(showPatternGenes)
+export(showPolygonSizeInfluence)
 export(showProcessingSteps)
 export(showSaveParameters)
 export(showSpatialCorFeats)
@@ -413,6 +429,7 @@ export(spatNetwDistributionsKneighbors)
 export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
+export(spatQueryGiottoPolygons)
 export(spatShift)
 export(spatUnit)
 export(spatialAEH)
@@ -429,6 +446,7 @@ export(subsetGiotto)
 export(subsetGiottoLocs)
 export(subsetGiottoLocsMulti)
 export(subsetGiottoLocsSubcellular)
+export(tessellate)
 export(trendSceek)
 export(updateGiottoImage)
 export(updateGiottoImageMG)
@@ -440,6 +458,7 @@ export(validObject)
 export(viewHMRFresults)
 export(viewHMRFresults2D)
 export(viewHMRFresults3D)
+export(viewHMRFresults_V2)
 export(violinPlot)
 export(writeGiottoLargeImage)
 export(writeHMRFresults)
@@ -465,6 +484,7 @@ exportMethods("[")
 exportMethods("[<-")
 exportMethods("activeFeatType<-")
 exportMethods("activeSpatUnit<-")
+exportMethods("ext<-")
 exportMethods("featType<-")
 exportMethods("instructions<-")
 exportMethods("objName<-")
@@ -476,8 +496,10 @@ exportMethods(centroids)
 exportMethods(colnames)
 exportMethods(copy)
 exportMethods(dim)
+exportMethods(ext)
 exportMethods(featIDs)
 exportMethods(featType)
+exportMethods(flip)
 exportMethods(instructions)
 exportMethods(ncol)
 exportMethods(nrow)
@@ -498,6 +520,7 @@ import(data.table)
 import(ggplot2)
 import(magrittr)
 import(utils)
+importClassesFrom(terra,SpatExtent)
 importFrom(graphics,segments)
 importFrom(magrittr,"%>%")
 importFrom(methods,"slot<-")
@@ -508,7 +531,10 @@ importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importMethodsFrom(Matrix,t)
+importMethodsFrom(terra,"ext<-")
 importMethodsFrom(terra,centroids)
+importMethodsFrom(terra,ext)
+importMethodsFrom(terra,flip)
 importMethodsFrom(terra,ncol)
 importMethodsFrom(terra,nrow)
 importMethodsFrom(terra,plot)

NEWS.md

@@ -1,5 +1,56 @@
 
 
+# Giotto Suite 3.3.1 (2023-08-02)
+
+## Breaking Changes
+- Change `checkGiottoEnvironment()`. Downgrade from error to message and return FALSE when a provided directory does not exist
+
+## Added
+- New file `poly_influence.R`
+- New function `showPolygonSizeInfluence()` within `poly_influence.R` to show if cells switch clusters when across resized polygon annotations 
+- New function `showCellProportionSwitchedPie()` within `poly_influence.R` to visualize results from `showPolygonSizeInfluence()` in a pie chart
+- New function `showCellProportionSwitchedSankey()` within `poly_influence.R` to visualize results from `showPolygonSizeInfluence()` in a Sankey diagram
+- New function `makePseudoVisium()` within `giotto_structure.R` to generate a pseudo visium grid of circular spots 
+- New function `tessellate()` within `giotto_structure.R` to generate a grid of hexagons or squares for spatial binning
+- New file `feature_set_enrichment.R`
+- New function `doFeatureSetEnrichment()` within `feature_set_enrichment.R` for GSEA analysis
+- New function `doGiottoClustree()` within `clustering.R` for visualizations of leiden clusters at varying resolutions
+- New `createArchRProj()` and `CreateGiottoObjectFromArchR()` functions to create a `giotto` object with ATAC or epigenetic features using the *ArchR* pipeline.
+- New `giottoMasterToSuite()` function to convert a `giotto` object created with the master version to a Giotto suite object.
+- New `readPolygonVizgenParquet()` for updated parquet outputs
+- Add *checkmate* to Imports for assertions checking
+- Add exported `create` function for `exprObj` creation
+- New file `spatial_manipulation.R`
+- Add `ext()` methods for `giottoPolygon`, `giottoPoints`, `spatialNetworkObj`, `spatLocsObj`, `giottoLargeImage`
+- Add `flip()` methods for `giottoPolygon`, `giottoPoints`, `spatialNetworkObj`, `spatLocsObj`, `SpatExtent`, `giottoLargeImage`
+- Add access to terra plotting params for `giottoLargeImage` `plot()` method.
+
+## Changes
+- Fix bug in `combine_matrices()`
+- Fix bug in `createGiottoObject()` that will not allow object creation without supplied expression information
+- Updated `polyStamp()` to replace an apply function with a crossjoin for better performance.
+- Updated `spatInSituPlotPoints()` with `plot_last` parameter. Default output now plots polygons above points for better visibility.
+- Add check for spatLocsObj for spatlocs in polyStamp()
+- Removed various print() and cat() statements throughout. 
+- Changed default verbose argument to FALSE for createGiottoObject
+- Changed default verbose argument to FALSE for joinGiottoObjects
+- Changed default verbose argument to FALSE for createGiottoObjectSubcellular
+- Default verbose = FALSE argument added to cellProximityEnrichmentSpots
+- Default verbose = FALSE argument added to specific_CCCScores_spots
+- Default verbose = FALSE argument added to runWNN
+- Default verbose = FALSE argument added to subset_giotto_points_object 
+- Default verbose = FALSE argument added to subset_feature_info_data 
+- Default verbose = FALSE argument added to subsetGiotto
+- Default verbose = FALSE argument added to subsetGiottoLocsSubcellular 
+- Default verbose = FALSE argument added to createGiottoXeniumObject_subcellular
+- Update `readPolygonFilesVizgenHDF5()` add option to return as `data.table` and skip `giottoPolygon` creation. Downstream `giottoPolygon` creation refactored as new internal function
+- Update cell segmentation workflow to check for *deepcell* and *PIL* python packages
+- Update cell segmentation workflow to return grayscale mask images instead of RGB
+- Update `createGiottoVisiumObject()` image h5 scalefactors reading to use partial matching for whether hi or lowres image is supplied
+- Update `giottoLargeImage` `plot()` method to use `terra::plot()` instead of `terra::plotRGB()` for grayscale images
+- Remove unnecessary prints from `subsetGiotto()`
+- Fix bug in `readCellMetadata()` and `readFeatMetadata()`
+
 
 # Giotto Suite 3.3.0 (2023-04-18)
 

R/NN_network.R

@@ -139,9 +139,24 @@ createNearestNetwork <- function(gobject,
                                         spat_unit = spat_unit,
                                         values = values,
                                         output = 'exprObj')
-
-    provenance = prov(expr_obj)
-    expr_values = expr_obj[] # extract matrix
+
+    if(!is.null(slot(gobject, 'h5_file'))) {
+      expr_path = slot(expr_values, 'exprMat')
+
+      expr_values = HDF5Array::h5mread(filepath = slot(gobject, 'h5_file'),
+                                       name = expr_path)
+
+      expr_dimnames = HDF5Array::h5readDimnames(filepath = slot(gobject, 'h5_file'),
+                                                name = expr_path)
+
+      rownames(expr_values) = expr_dimnames[[1]]
+      colnames(expr_values) = expr_dimnames[[2]]
+    } else {
+
+      provenance = prov(expr_obj)
+      expr_values = expr_obj[] # extract matrix
+
+    }
 
     # subset expression matrix
     if(!is.null(feats_to_use)) {
@@ -209,7 +224,7 @@ createNearestNetwork <- function(gobject,
   }
 
 
-print(nn_network_igraph) # debug
+
 
   # set default name
   if(is.null(name)) name = paste0(type, '.', dim_reduction_to_use)