Merge pull request #12 from alikhuseynov/seurat_v4

`readVizgen()` and `readXenium()`

.github/workflows/pkgdown.yaml

@@ -25,7 +25,7 @@ jobs:
       - name: Setup R and Bioconductor
         uses: grimbough/bioc-actions/setup-bioc@v1
         with:
-          bioc-version: 3.17
+          bioc-version: release
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

DESCRIPTION

@@ -6,6 +6,9 @@ Authors@R:
     c(person("Lambda", "Moses", email = "[email protected]", 
     role = c("aut", "cre"),
     comment = c(ORCID = "0000-0002-7092-9427")),
+    person("Alik", "Huseynov",
+    comment = c(ORCID = "0000-0002-1438-4389"),
+    role = "aut"),
     person("Lior", "Pachter", email = "[email protected]",
     role = c("aut", "ths"),
     comment = c(ORCID = "0000-0002-9164-6231")))
@@ -19,8 +22,10 @@ Imports:
     BiocGenerics,
     BiocNeighbors,
     BiocParallel,
+    data.table,
     DropletUtils,
     grDevices,
+    lifecycle,
     Matrix,
     methods,
     rjson,
@@ -61,14 +66,13 @@ Collate:
     'updateObject.R'
     'validity.R'
 Suggests: 
+    arrow,
     BiocStyle,
-    dplyr,
     knitr,
     rhdf5,
     rmarkdown,
     sfarrow,
     SFEData,
-    vroom,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Depends: 

NAMESPACE

@@ -44,7 +44,9 @@ export(.value2df)
 export(.warn_symbol_duplicate)
 export(ROIPoly)
 export(SFEVersion)
+export(SpatRasterImage)
 export(SpatialFeatureExperiment)
+export(addTxSpots)
 export(addVisiumSpotPoly)
 export(annotGeometries)
 export(annotGeometry)
@@ -57,6 +59,7 @@ export(annotOp)
 export(annotPred)
 export(annotSummary)
 export(bbox)
+export(callMeta)
 export(cellSeg)
 export(centroids)
 export(changeSampleIDs)
@@ -74,6 +77,7 @@ export(dimGeometry)
 export(dimGeometryNames)
 export(findSpatialNeighbors)
 export(findVisiumGraph)
+export(formatTxSpots)
 export(getImg)
 export(imgData)
 export(localResult)
@@ -84,7 +88,9 @@ export(localResults)
 export(mirror)
 export(nucSeg)
 export(read10xVisiumSFE)
+export(readCosMX)
 export(readVizgen)
+export(readXenium)
 export(removeEmptySpace)
 export(rowData)
 export(rowGeometries)
@@ -175,6 +181,7 @@ importFrom(S4Vectors,setValidity2)
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_elementMetadata<-")
 importFrom(SingleCellExperiment,"int_metadata<-")
+importFrom(SingleCellExperiment,counts)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_elementMetadata)
 importFrom(SingleCellExperiment,int_metadata)
@@ -195,6 +202,10 @@ importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
+importFrom(data.table,fread)
+importFrom(data.table,is.data.table)
+importFrom(data.table,merge.data.table)
+importFrom(data.table,rbindlist)
 importFrom(grDevices,col2rgb)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
@@ -217,6 +228,7 @@ importFrom(sf,"st_agr<-")
 importFrom(sf,"st_geometry<-")
 importFrom(sf,st_agr)
 importFrom(sf,st_area)
+importFrom(sf,st_as_sf)
 importFrom(sf,st_as_sfc)
 importFrom(sf,st_bbox)
 importFrom(sf,st_buffer)
@@ -261,11 +273,15 @@ importFrom(stats,median)
 importFrom(stats,setNames)
 importFrom(terra,"ext<-")
 importFrom(terra,ext)
+importFrom(terra,nlyr)
 importFrom(terra,rast)
 importFrom(terra,sources)
 importFrom(terra,unwrap)
 importFrom(terra,vect)
 importFrom(terra,wrap)
+importFrom(tools,file_ext)
+importFrom(tools,file_path_sans_ext)
 importFrom(utils,getFromNamespace)
+importFrom(utils,head)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)

R/SFE-class.R

@@ -192,8 +192,7 @@ SpatialFeatureExperiment <- function(assays,
                         spotDiameter, unit, BPPARAM) {
     if (is.null(colGeometries)) {
       cg_name <- if (is.na(spotDiameter)) "centroids" else "spotPoly"
-      colGeometries <- list(foo = .sc2cg(spatialCoords(spe), spotDiameter,
-                                         BPPARAM))
+      colGeometries <- list(foo = .sc2cg(spatialCoords(spe), spotDiameter, BPPARAM))
       names(colGeometries) <- cg_name
     }
     if (!is.null(rowGeometries)) {

R/coerce.R

@@ -36,8 +36,10 @@
 NULL
 
 .sc2cg <- function(coords_use, spotDiameter = NA, BPPARAM = SerialParam()) {
-    colnames(coords_use) <- c("x", "y")
-    cg_sfc <- df2sf(coords_use, spotDiameter = spotDiameter, BPPARAM = BPPARAM,
+    if (is.null(colnames(coords_use))) 
+        colnames(coords_use) <- paste0("V", seq_len(ncol(coords_use)))
+    cg_sfc <- df2sf(coords_use, spatialCoordsNames = colnames(coords_use),
+                    spotDiameter = spotDiameter, BPPARAM = BPPARAM,
                     geometryType = "POINT")
     rownames(cg_sfc) <- rownames(coords_use)
     cg_sfc