SpatialExperiment-methods {SpatialExperiment} | R Documentation |
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
.
## 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
x |
A |
spatialCoords |
Logical specifying whether to include columns from
|
value |
Replacement value for replacement methods. |
sample_id |
Logical value or character vector specifying sample
identifier(s) for |
image_id |
Logical value or character vector specifying image
identifier(s) for |
spatialData |
Logical specifying whether to include columns from
|
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
).
Return value varies depending on method, as described below.
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(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(x)
: Getter to return the imgData
DataFrame
.
imgData(x) <- value
: Setter to provide a DataFrame
object as imgData
of the SpatialExperiment
object.
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.
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)