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, colData = 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 replacement method for signature 'SpatialExperiment,'NULL''
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

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 arguments spatialCoords and colData, which can be used to include the columns of spatial coordinates (spatialCoords) and any additional columns from colData in the output DataFrame.

spatialData(x) <- value:

The spatialData setter expects a data.frame or DataFrame with the defined column names for the spatial coordinates. Spatial coordinate names can be set with the spatialCoordNames setter, and are set as c("x", "y") by default by the SpatialExperiment constructor. 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, colData="sample_id")

# 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
table(
  in_tissue = spe$in_tissue, 
  sample_id = spe$sample_id)