Methods for spatial attributes — SpatialExperiment-rotate-mirror • SpatialExperiment

The SpatialExperiment class provides methods to rotate and mirror SpatialExperiment objects and their spatialCoords.

Usage

# S4 method for class 'SpatialExperiment'
rotateCoords(x, sample_id = NULL, degrees = 90, warn = TRUE)

# S4 method for class 'SpatialExperiment'
mirrorCoords(x, sample_id = NULL, axis = c("h", "v"), warn = TRUE)

# S4 method for class 'SpatialExperiment'
rotateObject(x, sample_id = NULL, image_id = NULL, degrees = 90)

# S4 method for class 'SpatialExperiment'
mirrorObject(x, sample_id = NULL, image_id = NULL, axis = c("h", "v"))

Arguments

x: A SpatialExperiment object.
sample_id: Logical value or character vector specifying sample identifier(s) for scaleFactors. Default = TRUE (all samples).
degrees: single numeric in +/-[0,90,...,360] specifying how many degrees to rotate. A negative/positive value corresponds to counter-/clockwise rotation. Applicable for rotateCoords and rotateObject methods.
warn: Logical value indicating whether to print a warning about mismatches between coordinates and images, possible with the spatialCoords transformation methods rotateCoords and mirrorCoords.
axis: character string specifying whether to mirror horizontally ("h") or vertically ("v"). Applicable for mirrorCoords and mirrorObject methods.
image_id: Logical value or character vector specifying image identifier(s) for scaleFactors. Default = TRUE (all images).

Value

Return value varies depending on method, as described below.

Details

Additional details for each type of data attribute are provided below.

spatialCoords transformation methods

rotateCoords(x, sample_id, degrees, warn):: Apply a rotation to the spatialCoords of x, potentially subsetted to sample sample_id (or without subsetting if sample_id is NULL), by the specified number of degrees clockwise. Warn about mismatches with images if warn.
mirrorCoords(x, sample_id, axis, warn):: Reflect the spatialCoords of x across either the horizontal or vertical axis, specified by supplying "h" or "v" to the axis argument, respectively. Subset x to just the sample sample_id, if not NULL. Warn about mismatches with images if warn.

SpatialExperiment transformation wrapper methods

rotateObject(x, sample_id, image_id, degrees):: Apply a rotation to the spatialCoords and imgData of x, potentially subsetted to sample sample_id (or without subsetting if sample_id is NULL), by the specified number of degrees clockwise. Wrapper around rotateCoords and rotateImg.
mirrorObject(x, sample_id, image_id, axis):: Reflect the spatialCoords and imgData of x across either the horizontal or vertical axis, specified by supplying "h" or "v" to the axis argument, respectively. Subset x to just the sample sample_id, if not NULL. Wrapper around mirrorCoords and mirrorImg.

Author

Nicholas J. Eagles

Examples

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] "/tmp/RtmppdZi9A/temp_libpathcf263c794d1/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

# rotateCoords(), mirrorCoords(), rotateObject(), and mirrorObject() return a
# SpatialExperiment, potentially subsetted by sample.

# Subset to just "section1"; rotate coordinates 90 degrees clockwise followed
# by a reflection across the vertical axis
spe_coords <- rotateCoords(spe, sample_id = "section1", degrees = 90)
#> Warning: Invoking 'rotateCoords' or 'rotateImg' independently may result in mismatches between coordinates and images. Please use 'rotateObject' to ensure consistency.
spe_coords <- mirrorCoords(spe_coords, axis = "v")
#> Warning: Invoking 'mirrorCoords' or 'mirrorImg' independently may result in mismatches between coordinates and images. Please use 'mirrorObject' to ensure consistency.

# Subset to just "section2"; transform both the imgData() and spatialCoords()
# by a 180-degree rotation then reflection across the vertical axis
spe_wrapper <- rotateObject(spe, sample_id = "section2", degrees = 180)
spe_wrapper <- mirrorObject(spe_wrapper, axis = "v")