SpatialExperiment-methods {SpatialExperiment}

R Documentation

Methods for spatial attributes

Description

The SpatialExperiment class provides a family of methods to get and set spatial data attributes in SpatialExperiment objects. Spatial attributes include spatialData, spatialCoords, imgData, and scaleFactors.

Usage

## S4 method for signature 'SpatialExperiment'
spatialData(x, spatialCoords = FALSE)

## S4 replacement method for signature 'SpatialExperiment,DFrame'
spatialData(x) <- value

## S4 replacement method for signature 'SpatialExperiment,'NULL''
spatialData(x) <- value

## S4 method for signature 'SpatialExperiment'
spatialDataNames(x)

## S4 replacement method for signature 'SpatialExperiment,character'
spatialDataNames(x) <- value

## S4 method for signature 'SpatialExperiment'
spatialCoords(x)

## S4 replacement method for signature 'SpatialExperiment,matrix'
spatialCoords(x) <- value

## S4 replacement method for signature 'SpatialExperiment,'NULL''
spatialCoords(x) <- value

## S4 method for signature 'SpatialExperiment'
spatialCoordsNames(x)

## S4 replacement method for signature 'SpatialExperiment,character'
spatialCoordsNames(x) <- value

## S4 replacement method for signature 'SpatialExperiment,'NULL''
spatialCoordsNames(x) <- value

## S4 method for signature 'SpatialExperiment'
scaleFactors(x, sample_id = TRUE, image_id = TRUE)

## S4 method for signature 'SpatialExperiment'
imgData(x)

## S4 replacement method for signature 'SpatialExperiment,DataFrame'
imgData(x) <- value

## S4 replacement method for signature 'SpatialExperiment,'NULL''
imgData(x) <- value

Arguments

x	A SpatialExperiment object.
spatialCoords	Logical specifying whether to include columns from spatialCoords in the output DataFrame from spatialData. Default = FALSE.
value	Replacement value for replacement methods.
sample_id	Logical value or character vector specifying sample identifier(s) for scaleFactors. Default = TRUE (all samples).
image_id	Logical value or character vector specifying image identifier(s) for scaleFactors. Default = TRUE (all images).
spatialData	Logical specifying whether to include columns from spatialData in the output DataFrame from colData. Default = FALSE

Details

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

spatialData and spatialCoords are distinguished as follows: spatialData is a DataFrame containing all the data associated with the spatial information (optionally including spatial coordinates from spatialCoords), while spatialCoords is a numeric matrix containing only the defined spatial coordinates (e.g. columns x and y).

Value

Return value varies depending on method, as described below.

spatialData and spatialCoords methods

spatialData(x):

The spatialData getter provides the optional argument spatialCoords, which can be used to include the columns of spatial coordinates (spatialCoords) in the output DataFrame.

spatialData(x) <- value:

The spatialData setter expects a DataFrame. If the input does not contain an in_tissue column, this will be included with a default value of 1.

spatialCoords(x):

Getter for numeric matrix of spatial coordinates.

spatialCoords(x) <- value:

Setter for numeric matrix of spatial coordinates.

spatialDataNames and spatialCoordsNames methods

spatialDataNames(x):

Returns the column names of the spatialData DataFrame.

spatialDataNames(x) <- value:

Setter to replace column names in the spatialData DataFrame.

spatialCoordsNames(x):

Returns the defined names of the spatial coordinates (e.g. c("x", "y")).

spatialCoordsNames(x) <- value:

Setter to define the names of the spatial coordinate columns.

imgData methods

imgData(x):

Getter to return the imgData DataFrame.

imgData(x) <- value:

Setter to provide a DataFrame object as imgData of the SpatialExperiment object.

Other methods

scaleFactors(x, sample_id, image_id):

Getter to return the scale factors associated with the sample_id(s) and image_id(s) provided. This is related to the stored image(s) in the SpatialExperiment imgData structure. See argument descriptions for further details.

Examples

example(read10xVisium)

# spatialData returns a DataFrame
spatialData(spe)

# spatialCoords returns a numeric matrix
head(spatialCoords(spe))

# spatialData replacement method
spdata <- spatialData(spe)
spdata$array_col <- spdata$array_row
spatialData(spe) <- spdata

# return additional columns for spatialData
spatialData(spe, spatialCoords=TRUE)

# change spatial coordinate names
spatialCoordsNames(spe)
spatialCoordsNames(spe) <- c("x", "y")
head(spatialCoords(spe))

# imgData and scale factors
imgData(spe)
scaleFactors(spe)

# tabulate number of spots mapped to tissue
cd <- colData(spe, spatialData = TRUE)
table(
  in_tissue = cd$in_tissue, 
  sample_id = cd$sample_id)

---