Package 'alabaster.sfe'

Read BioFormatsImage from alabaster on disk representation

Description

Reads the metadata and imgSource will point to the file within the on disk representation of SFE. The image itself should not be moved or the BioFormatsImabe object will no longer work.

Usage

readBioFormatsImage(path, metadata = NULL, ...)

Arguments

path	String containing a path to a directory, itself created with a saveObject method.
metadata	Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).
...	Ignored, but used for other methods.

Value

A BioFormatsImage object for SFE.

See Also

Other readObject-SFE-image: readExtImage(), readSpatRaster()

Examples

library(SFEData)
fp <- tempfile()
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
x2 <- XeniumOutput("v2", file_path = file.path(fp, "xenium2"))

# Single file OME-TIFF
fsave <- file.path(fp, "bfi1")
sfe <- readXenium(x1)
bfi <- getImg(sfe)
bfi <- affineImg(bfi, M = matrix(c(cos(pi/6), sin(pi/6), -sin(pi/6), cos(pi/6)), nrow = 2), 
                 v = c(0,0))
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)

unlink(fsave, recursive = TRUE)

# Multi file OME-TIFF
fsave <- file.path(fp, "bfi2")
sfe <- readXenium(x2)
bfi <- getImg(sfe)
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)

---

Read ExtImage from disk

Description

Read ExtImage from disk

Usage

readExtImage(path, metadata = NULL, ...)

Arguments

path	String containing a path to a directory, itself created with a saveObject method.
metadata	Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).
...	Arguments passed to readImage.

Value

A ExtImage object for SFE.

See Also

Other readObject-SFE-image: readBioFormatsImage(), readSpatRaster()

Examples

library(SFEData)
fp <- tempfile()
fsave <- file.path(fp, "exi")
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
sfe <- readXenium(x1)
bfi <- getImg(sfe)
exi <- toExtImage(bfi)
saveObject(exi, fsave)
exi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)

---

Read sf from alabaster on disk representation

Description

Read the GeoParquet file into R. GeoParquet should also work in any programming language that supports arrow. Newer version of GDAL with Parquet driver is not strictly necessary if the geometry's WKB can be converted to whichever language specific object such as sfc in R.

Usage

readSF(path, metadata = NULL)

Arguments

path	String containing a path to a directory, itself created with a saveObject method.
metadata	Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).

Value

An sf data frame

Examples

library(sf)
fp <- tempfile()
df <- as.data.frame(matrix(rnorm(10), ncol = 2))
df <- st_as_sf(df, coords = names(df), crs = NA)
saveObject(df, path = fp)
df2 <- readObject(fp)

---

Read SFE object from alabaster on disk representation

Description

Read SFE object from alabaster on disk representation

Usage

readSpatialFeatureExperiment(path, metadata = NULL, ...)

Arguments

path	String containing a path to a directory, itself created with a saveObject method.
metadata	Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).
...	Further arguments to pass to individual methods.

Value

A SpatialFeatureExperiment object

Examples

library(SFEData)
fp <- tempfile()
fn <- file.path(fp, "vizgen")
d <- VizgenOutput(dataset = "cellpose", file_path = fn)
suppressWarnings(sfe <- readVizgen(d))
fsave <- file.path(fp, "sfe_save")
saveObject(sfe, fsave)
sfe2 <- readObject(fsave)

---

Read SpatRaster from alabaster on disk representation

Description

Not the same as terra::rast; here this function also reads the metadata file.

Usage

readSpatRaster(path, metadata = NULL, ...)

Arguments

path	String containing a path to a directory, itself created with a saveObject method.
metadata	Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).
...	Arguments passed to rast, character method.

Value

A SpatRasterImage object for SFE.

See Also

Other readObject-SFE-image: readBioFormatsImage(), readExtImage()

Examples

library(SFEData)
fp <- tempfile()
fn <- file.path(fp, "vizgen")
d <- VizgenOutput(dataset = "cellpose", file_path = fn)
suppressWarnings(sfe <- readVizgen(d))
img <- getImg(sfe)
class(img)
fsave <- file.path(fp, "img")
saveObject(img, fsave)
img2 <- readObject(fsave)

---

Save BioFormatsImage for alabaster

Description

This function copies the original file to a pre-defined location within the directory that stores the on disk representation of the SFE object for data sharing. Since BioFormatsImage is essentially just some metadata in memory and it never loads the image into memory (once the image is loaded into memory it becomes ExtImage), once the original image is moved, the BioFormatsImage object will no longer work, which is why the pre-defined location is important. This function also saves the metadata, which includes spatial extent and affine transformations.

Usage

## S4 method for signature 'BioFormatsImage'
saveObject(x, path, ...)

Arguments

x	A Bioconductor object of the specified class.
path	String containing the path to a directory in which to save x.
...	Ignored

Value

x is saved into path and NULL is invisibly returned.

See Also

Other saveObject-SFE-image: saveObject,ExtImage-method, saveObject,SpatRaster-method

Examples

library(SFEData)
fp <- tempfile()
fsave <- file.path(fp, "bfi2")
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
sfe <- readXenium(x1)
bfi <- getImg(sfe)
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)

---

Save ExtImage to disk for alabaster

Description

Save ExtImage to disk for alabaster

Usage

## S4 method for signature 'ExtImage'
saveObject(x, path, ...)

Arguments

x	A Bioconductor object of the specified class.
path	String containing the path to a directory in which to save x.
...	Extra arguments passed to writeImage.

Value

x is saved into path and NULL is invisibly returned.

See Also

Other saveObject-SFE-image: saveObject,BioFormatsImage-method, saveObject,SpatRaster-method

Examples

library(SFEData)
fp <- tempfile()
fsave <- file.path(fp, "exi")
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
sfe <- readXenium(x1)
bfi <- getImg(sfe)
exi <- toExtImage(bfi)
saveObject(exi, fsave)
exi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)

---

Save sf to disk for alabaster

Description

sf data frames are saved as GeoParquet.

Usage

## S4 method for signature 'sf'
saveObject(x, path)

Arguments

x	A Bioconductor object of the specified class.
path	String containing the path to a directory in which to save x.

Value

x is saved into path and NULL is invisibly returned.

Examples

library(sf)
fp <- tempfile()
df <- as.data.frame(matrix(rnorm(10), ncol = 2))
df <- st_as_sf(df, coords = names(df), crs = NA)
saveObject(df, path = fp)

---

Save a SpatialFeatureExperiment object

Description

Save SFE objects to disk in an interoperable, language agnostic format that may also facilitate out of memory operations via HDF5 (non-spatial, inherited from alabaster.sce) and Apache Parquet (geometries).

Usage

## S4 method for signature 'SpatialFeatureExperiment'
saveObject(x, path, ...)

Arguments

x	A Bioconductor object of the specified class.
path	String containing the path to a directory in which to save x.
...	Additional named arguments to pass to specific methods.

Details

There's no new arguments for ... for the SFE, SpatialExperiment, and SingleCellExperiment methods, but there is an argument that can be specified for ... in the SummarizedExperiment method of saveObject.

At present, spatial results in featureData for geometries and dimension reductions (see colFeatureData) and parameters of spatial analyses (see getParams) are not save because those parts of the SFE object are more experimental and are subject to change. colFeatureData where global spatial results are stored for columns of colData(x) is saved by the alabaster saveObject method for DataFrame.

Value

x is saved into path and NULL is invisibly returned.

Examples

library(SpatialFeatureExperiment)
library(Voyager)
library(SFEData)
library(SingleCellExperiment)
library(scater)

fp <- tempfile()
fn <- file.path(fp, "vizgen")
d <- VizgenOutput(dataset = "cellpose", file_path = fn)
suppressWarnings(sfe1 <- readVizgen(d, add_molecules = TRUE))

colGraph(sfe1, "knn5") <- findSpatialNeighbors(sfe1, method = "knearneigh", k = 5)
SpatialFeatureExperiment::centroids(sfe1)$foo <- rnorm(ncol(sfe1))
sfe1 <- logNormCounts(sfe1)
sfe1 <- runMoransI(sfe1, colGraphName = "knn5")
sfe1 <- colDataMoransI(sfe1, features = c("transcript_count", "anisotropy", 
                                          "perimeter_area_ratio", "solidity"))
sfe1 <- colGeometryMoransI(sfe1, colGeometryName = "centroids", features = "foo")
sfe1 <- runPCA(sfe1, ncomponents = 10)
sfe1 <- reducedDimMoransI(sfe1, components = 1:10)

sfe1 <- runUnivariate(sfe1, type = "localmoran", features = rownames(sfe1)[1])

fsave <- file.path(fp, "sfe_vizgen")
saveObject(sfe1, fsave)
sfe2 <- readObject(fsave)

unlink(fsave, recursive = TRUE)

---

Save SpatRaster to disk for alabaster

Description

Intended for SpatRasterImage which really is SpatRaster that also inherits from SPE's SpatialImage. Besides writeRaster, this function also writes a metadata file in the alabaster framework. If the image is not loaded into memory and the original file is already spatially registered, e.g. it has a spatial extent, then the original file is copied to a pre-defined place in the on-disk representation of SFE and writeRaster is not called.

Usage

## S4 method for signature 'SpatRaster'
saveObject(x, path, ...)

Arguments

x	A Bioconductor object of the specified class.
path	String containing the path to a directory in which to save x.
...	Extra parameters passed to writeRaster.

Value

x is saved into path and NULL is invisibly returned.

See Also

Other saveObject-SFE-image: saveObject,BioFormatsImage-method, saveObject,ExtImage-method

Examples

library(SFEData)
fp <- tempfile()
fn <- file.path(fp, "vizgen")
d <- VizgenOutput(dataset = "cellpose", file_path = fn)
suppressWarnings(sfe <- readVizgen(d))
img <- getImg(sfe)
class(img)
fsave <- file.path(fp, "img")
saveObject(img, fsave)
img2 <- readObject(fsave)

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