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SpatialFeatureExperiment coercion methods

Source: R/coerce.R
SpatialFeatureExperiment-coercion.Rd

The SpatialFeatureExperiment class inherits from SpatialExperiment, which in turn inherits from SingleCellExperiment. A SpatialExperiment object with geometries in colGeometries in the int_colData, rowGeometries in the int_elementMetadata, or annotGeometries in the int_metadata can be directly converted to SpatialFeatureExperiment with as(spe, "SpatialFeatureExperiment"). A SpatialExperiment object without the geometries can also be converted; the coordinates in the spatialCoords field will be used to make POINT geometries named "centroids" to add to colGeometries. The geometries can also be supplied separately when using toSpatialFeatureExperiment. Images are converted to SpatRaster.

Usage

# S4 method for class 'SpatialExperiment'
toSpatialFeatureExperiment(
  x,
  colGeometries = NULL,
  rowGeometries = NULL,
  annotGeometries = NULL,
  spatialCoordsNames = c("x", "y"),
  annotGeometryType = "POLYGON",
  spatialGraphs = NULL,
  spotDiameter = NA,
  unit = NULL
)

# S4 method for class 'SingleCellExperiment'
toSpatialFeatureExperiment(
  x,
  sample_id = "sample01",
  spatialCoordsNames = c("x", "y"),
  spatialCoords = NULL,
  colGeometries = NULL,
  rowGeometries = NULL,
  annotGeometries = NULL,
  annotGeometryType = "POLYGON",
  spatialGraphs = NULL,
  spotDiameter = NA,
  scaleFactors = 1,
  imageSources = NULL,
  image_id = NULL,
  loadImage = TRUE,
  imgData = NULL,
  unit = NULL
)

# S4 method for class 'Seurat'
toSpatialFeatureExperiment(
  x,
  add_molecules = TRUE,
  flip = c("geometry", "image", "none"),
  image_scalefactors = c("lowres", "hires"),
  unit = NULL,
  BPPARAM = SerialParam()
)

Arguments

x

A SpatialExperiment or Seurat object to be coerced to a SpatialFeatureExperiment object.

colGeometries

Geometry of the entities that correspond to the columns of the gene count matrix, such as cells and Visium spots. It must be a named list of one of the following:

An sf data frame

The geometry column specifies the geometry of the entities.

An ordinary data frame specifying centroids

Column names for the coordinates are specified in the spatialCoordsNames argument. For Visium and ST, in addition to the centroid coordinate data frame, the spot diameter in the same unit as the coordinates can be specified in the spotDiamter argument.

An ordinary data frame specifying polygons

Also use spatialCoordsNames. There should an additional column "ID" to specify which vertices belong to which polygon. The coordinates should not be in list columns. Rather, the data frame should look like it is passed to ggplot2::geom_polygon. If there are holes, then there must also be a column "subID" that differentiates between the outer polygon and the holes.

In all cases, the data frame should specify the same number of geometries as the number of columns in the gene count matrix. If the column "barcode" is present, then it will be matched to column names of the gene count matrix. Otherwise, the geometries are assumed to be in the same order as columns in the gene count matrix. If the geometries are specified in an ordinary data frame, then it will be converted into sf internally. Named list of data frames because each entity can have multiple geometries, such as whole cell and nuclei segmentations. The geometries are assumed to be POINTs for centroids and POLYGONs for segmentations. If polygons are specified in an ordinary data frame, then anything with fewer than 3 vertices will be removed. For anything other than POINTs, attributes of the geometry will be ignored.

rowGeometries

Geometry associated with genes or features, which correspond to rows of the gene count matrix.

annotGeometries

Geometry of entities that do not correspond to columns or rows of the gene count matrix, such as tissue boundary and pathologist annotations of histological regions, and nuclei segmentation in a Visium dataset. Also a named list as in colGeometries. The ordinary data frame may specify POINTs, POLYGONs, or LINESTRINGs, or their MULTI versions. Each data frame can only specify one type of geometry. For MULTI versions, there must be a column "group" to identify each MULTI geometry.

spatialCoordsNames

A character vector of column names if *Geometries arguments have ordinary data frames, to identify the columns in the ordinary data frames that specify the spatial coordinates. If colGeometries is not specified, then this argument will behave as in SpatialExperiment, but colGeometries will be given precedence if provided.

annotGeometryType

Character vector specifying geometry type of each element of the list if annotGeometry is specified. Each element of the vector must be one of POINT, LINESTRING, POLYGON, MULTIPOINT, MULTILINESTRING, and MULTIPOLYGON. Must be either length 1 (same for all elements of the list) or the same length as the list. Ignored if the corresponding element is an sf object.

spatialGraphs

A named list of listw objects (see spdep) for spatial neighborhood graphs.

spotDiameter

Spot diameter for technologies with arrays of spots of fixed diameter per slide, such as Visium, ST, DBiT-seq, and slide-seq. The diameter must be in the same unit as the coordinates in the *Geometry arguments. Ignored for geometries that are not POINT or MULTIPOINT.

unit

# Default unit is "micron". However for Visium one can choose between "micron" or "full_res_image_pixel".

sample_id

A character sample identifier, which matches the sample_id in imgData. The sample_id will also be stored in a new column in colData, if not already present. Default = sample01.

spatialCoords

A numeric matrix containing columns of spatial coordinates, as in SpatialExperiment. The coordinates are centroids of the entities represented by the columns of the gene count matrix. If colGeometries is also specified, then it will be given priority and a warning is issued. Otherwise, the sf representation of the centroids will be stored in the colGeometry called centroids.

scaleFactors

Optional scale factors associated with the image(s). This can be provided as a numeric value, numeric vector, list, or file path to a JSON file for the 10x Genomics Visium platform. For 10x Genomics Visium, the correct scale factor will automatically be selected depending on the resolution of the image from imageSources. Default = 1.

imageSources

Optional file path(s) or URL(s) for one or more image sources.

image_id

Optional character vector (same length as imageSources) containing unique image identifiers.

loadImage

Logical indicating whether to load image into memory. Default = FALSE.

imgData

Optional DataFrame containing the image data. Alternatively, this can be built from the arguments imageSources and image_id (see Details).

add_molecules

Logical, whether to add transcripts coordinates to an object.

flip

To flip the image, geometry coordinates, or none. Because the image has the origin at the top left while the geometry has origin at the bottom left, one of them needs to be flipped for them to match. If one of them is already flipped, then use "none". The image will not be flipped if it's GeoTIFF.

image_scalefactors

# A character, choose between "lowres" or "hires". Only for 10X Visium, image scaling factors are from `scalefactors_json.json` file.

BPPARAM

Deprecated when coercing from SpatialExperiment, but is used when coercing from Seurat object.

Value

A SpatialFeatureExperiment object

Examples

library(SpatialExperiment)
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: ‘BiocGenerics’
#> The following object is masked from ‘package:SpatialFeatureExperiment’:
#> 
#>     saveRDS
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> 
#> Attaching package: ‘IRanges’
#> The following objects are masked from ‘package:EBImage’:
#> 
#>     resize, tile
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#> 
#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     anyMissing, rowMedians
#> The following object is masked from ‘package:EBImage’:
#> 
#>     channel
example(read10xVisium)
#> 
#> rd10xV> dir <- system.file(
#> rd10xV+   file.path("extdata", "10xVisium"), 
#> rd10xV+   package = "SpatialExperiment")
#> 
#> rd10xV> sample_ids <- c("section1", "section2")
#> 
#> rd10xV> samples <- file.path(dir, sample_ids, "outs")
#> 
#> rd10xV> list.files(samples[1])
#> [1] "raw_feature_bc_matrix" "spatial"              
#> 
#> rd10xV> list.files(file.path(samples[1], "spatial"))
#> [1] "scalefactors_json.json"    "tissue_lowres_image.png"  
#> [3] "tissue_positions_list.csv"
#> 
#> rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
#> [1] "/home/runner/work/_temp/Library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"
#> 
#> rd10xV> (spe <- read10xVisium(samples, sample_ids, 
#> rd10xV+   type = "sparse", data = "raw", 
#> rd10xV+   images = "lowres", load = FALSE))
#> class: SpatialExperiment 
#> dim: 50 99 
#> metadata(0):
#> assays(1): counts
#> rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
#>   ENSMUSG00000005886 ENSMUSG00000101476
#> rowData names(1): symbol
#> colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#>   AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
#> colData names(4): in_tissue array_row array_col sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor
#> 
#> rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
#> rd10xV> samples2 <- file.path(dir, sample_ids)
#> 
#> rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
#> rd10xV+   type = "sparse", data = "raw", 
#> rd10xV+   images = "lowres", load = FALSE))
#> class: SpatialExperiment 
#> dim: 50 99 
#> metadata(0):
#> assays(1): counts
#> rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
#>   ENSMUSG00000005886 ENSMUSG00000101476
#> rowData names(1): symbol
#> colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#>   AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
#> colData names(4): in_tissue array_row array_col sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor
#> 
#> rd10xV> # tabulate number of spots mapped to tissue
#> rd10xV> cd <- colData(spe)
#> 
#> rd10xV> table(
#> rd10xV+   in_tissue = cd$in_tissue, 
#> rd10xV+   sample_id = cd$sample_id)
#>          sample_id
#> in_tissue section1 section2
#>     FALSE       28       27
#>     TRUE        22       22
#> 
#> rd10xV> # view available images
#> rd10xV> imgData(spe)
#> DataFrame with 2 rows and 4 columns
#>     sample_id    image_id   data scaleFactor
#>   <character> <character> <list>   <numeric>
#> 1    section1      lowres   ####   0.0510334
#> 2    section2      lowres   ####   0.0510334
# There can't be duplicate barcodes
colnames(spe) <- make.unique(colnames(spe), sep = "-")
rownames(spatialCoords(spe)) <- colnames(spe)
sfe <- toSpatialFeatureExperiment(spe)
# For coercing Seurat to SFE see this -> ./vignettes/seurat_sfe_coerce.Rmd