SpatialImage-methods: `SpatialImage` methods

Description

Methods defined on the SpatialImage class. Some of these methods must be overridden in order to ensure proper functionality of the derived classes (see Required methods below). Other methods are designed to work across all SpatialImage-derived subclasses, and should only be overridden if necessary

Usage

# S3 method for SpatialImage
Cells(x)
# S3 method for SpatialImage
DefaultAssay(object, ...)
# S3 method for SpatialImage
DefaultAssay(object, ...) <- value
# S3 method for SpatialImage
GetImage(object, mode = c("grob", "raster", "plotly", "raw"), ...)
# S3 method for SpatialImage
GetTissueCoordinates(object, ...)
# S3 method for SpatialImage
IsGlobal(object, ...)
# S3 method for SpatialImage
Key(object, ...)
# S3 method for SpatialImage
Key(object, ...) <- value
# S3 method for SpatialImage
Radius(object)
# S3 method for SpatialImage
RenameCells(object, new.names = NULL, ...)
# S3 method for SpatialImage
[(x, i, ...)
# S3 method for SpatialImage
dim(x)
# S3 method for SpatialImage
subset(x, cells, ...)
# S4 method for SpatialImage
show(object)

Arguments

x, object

A SpatialImage-derived object

...

Arguments passed to other methods

value

Depends on the method:

DefaultAssay<-: Assay that the image should be associated with
Key<-: New key for the image

mode

How to return the image; should accept one of “grob”, “raster”, “plotly”, or “raw”

new.names

vector of new cell names

i, cells

A vector of cells to keep

Value

[Override] Cells: should return cell names

DefaultAssay: The associated assay of a SpatialImage-derived object

DefaultAssay<-: object with the associated assay updated

[Override] GetImage: The image data from a SpatialImage-derived object

[Override] GetTissueCoordinates: ...

IsGlobal: returns TRUE as images are, by default, global

Key: The key for a SpatialImage-derived object

Key<-: object with the key set to value

Radius: The spot radius size; by default, returns NULL

[Override] RenameCells: object with the new cell names

[, subset: x/object for only the cells requested

[Override] dim: The dimensions of the image data in (Y, X) format

show: Prints summary to stdout and invisibly returns NULL

Functions

Cells.SpatialImage: Get the cell names from an image ([Override])
DefaultAssay.SpatialImage: Get the associated assay of a SpatialImage-derived object
DefaultAssay<-.SpatialImage: Set the associated assay of a SpatialImage-derived object
GetImage.SpatialImage: Get the image data from a SpatialImage-derived object
GetTissueCoordinates.SpatialImage: Get tissue coordinates for a SpatialImage-derived object ([Override])
IsGlobal.SpatialImage: Globality test for SpatialImage-derived object
Key.SpatialImage: Get the key for a SpatialImage-derived object
Key<-.SpatialImage: Set the key for a SpatialImage-derived object
Radius.SpatialImage: Get the spot radius size
RenameCells.SpatialImage: Rename cells in a SpatialImage-derived object ([Override])
[.SpatialImage: Subset a SpatialImage-derived object
dim.SpatialImage: Get the plotting dimensions of an image ([Override])
subset.SpatialImage: Subset a SpatialImage-derived object ([Override])
show,SpatialImage-method: Overview of a SpatialImage-derived object

Provided methods

These methods are defined on the SpatialImage object and should not be overridden without careful thought

DefaultAssay and DefaultAssay<-
Key and Key<-
GetImage; this method can be overridden to provide image data, normally returns empty image data. If overridden, should default to returning a grob object
IsGlobal
Radius; this method can be overridden to provide a spot radius for image objects
[; this method can be overridden to change default subset behavior, normally returns subset(x = x, cells = i). If overridden, should only accept i

Required methods

All subclasses of the SpatialImage class must define the following methods; simply relying on the SpatialImage method will result in errors. For required parameters and their values, see the Usage and Arguments sections

Cells: Return the cell/spot barcodes associated with each position
dim: Return the dimensions of the image for plotting in (Y, X) format
GetTissueCoordinates: Return tissue coordinates; by default, must return a two-column data.frame with x-coordinates in the first column and y-coordinates in the second
Radius: Return the spot radius; returns NULL by default for use with non-spot image technologies
RenameCells: Rename the cell/spot barcodes for this image
subset: Subset the image data by cells/spots

These methods are used throughout Seurat, so defining them and setting the proper defaults will allow subclasses of SpatialImage to work seamlessly