Spatial graph methods

Spatial neighborhood graphs as spdep's listw objects are stored in the int_metadata of the SFE object. The listw class is used because spdep has many useful methods that rely on the neighborhood graph as listw. See the spdep doumentation website for functions to edit the spatial neighborhood graph, or the nb object within the listw.

Usage

# S4 method for class 'SpatialFeatureExperiment'
spatialGraphs(x, MARGIN = NULL, sample_id = "all", name = "all")

colGraphs(x, sample_id = "all", name = "all")

rowGraphs(x, sample_id = "all", name = "all")

annotGraphs(x, sample_id = "all", name = "all")

# S4 method for class 'SpatialFeatureExperiment'
spatialGraphs(x, MARGIN = NULL, sample_id = "all", name = "all") <- value

colGraphs(x, sample_id = "all", name = "all") <- value

rowGraphs(x, sample_id = "all", name = "all") <- value

annotGraphs(x, sample_id = "all", name = "all") <- value

# S4 method for class 'SpatialFeatureExperiment,numeric'
spatialGraphNames(x, MARGIN, sample_id = 1L)

# S4 method for class 'SpatialFeatureExperiment,numeric,ANY,character'
spatialGraphNames(x, MARGIN, sample_id = 1L) <- value

colGraphNames(x, sample_id = 1L)

rowGraphNames(x, sample_id = 1L)

annotGraphNames(x, sample_id = 1L)

colGraphNames(x, sample_id = 1L) <- value

rowGraphNames(x, sample_id = 1L) <- value

annotGraphNames(x, sample_id = 1L) <- value

# S4 method for class 'SpatialFeatureExperiment'
spatialGraph(x, type = 1L, MARGIN, sample_id = 1L)

colGraph(x, type = 1L, sample_id = 1L)

rowGraph(x, type = 1L, sample_id = 1L)

annotGraph(x, type = 1L, sample_id = 1L)

# S4 method for class 'SpatialFeatureExperiment'
spatialGraph(x, type = 1L, MARGIN, sample_id = NULL) <- value

colGraph(x, type = 1L, sample_id = 1L) <- value

rowGraph(x, type = 1L, sample_id = 1L) <- value

annotGraph(x, type = 1L, sample_id = 1L) <- value

Arguments

x

A SpatialFeatureExperiment object.

MARGIN

As in apply. 1 stands for rows and 2 stands for columns. In addition, 3 stands for spatial neighborhood graphs that correspond to annotGeometries.

sample_id

Name of the sample the graph is associated with. This is useful when multiple pieces of tissues are in the same SFE object (say for a joint dimension reduction and clustering) and the spatial neighborhood is only meaningful within the same piece of tissue. See the sample_id argument in SpatialExperiment.

name

Name of the graphs to add to each sample_id; used in the spatialGraphs replacement method as it must be character while type can be either an integer index or a name.

value

A listw object (*Graph), or a named list of list of listw objects (*Graphs) where the names of the top level list are sample_ids when adding graphs for all samples in the margin of interest, or a list of listw objects when adding graphs for one sample in one margin.

type

An integer specifying the index or string specifying the name of the *Graph to query or replace. If missing, then the first item in the *Graph will be returned or replaced.

Value

Getters for multiple graphs return a named list. Getters for names return a character vector of the names. Getters for single graphs return a listw object. Setters return an SFE object.

Examples

library(SFEData)
sfe <- McKellarMuscleData(dataset = "small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
g1 <- findVisiumGraph(sfe)
g2 <- findSpatialNeighbors(sfe)

# Set all graphs of a margin by a named list
spatialGraphs(sfe, MARGIN = 2L, sample_id = "Vis5A") <-
    list(tri2nb = g2, visium = g1)
# Or equivalently
colGraphs(sfe, sample_id = "Vis5A") <- list(tri2nb = g2, visium = g1)

# Get all graphs of a margin, returning a named list
gs <- spatialGraphs(sfe, MARGIN = 2L)
# Or equivalently
gs <- colGraphs(sfe)

# Set graph of the same name and same margin for multiple samples
# Each sample has a separate graph
sfe2 <- McKellarMuscleData("small2")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
sfe_combined <- cbind(sfe, sfe2)
colGraphs(sfe_combined, name = "visium", sample_id = "all") <-
    findVisiumGraph(sfe_combined, sample_id = "all")

# Get graph names
spatialGraphNames(sfe, MARGIN = 2L, sample_id = "Vis5A")
#> [1] "tri2nb" "visium"
# Or equivalently (sample_id optional as only one sample is present)
colGraphNames(sfe)
#> [1] "tri2nb" "visium"

# Set graph names
spatialGraphNames(sfe, MARGIN = 2L) <- c("foo", "bar")
colGraphNames(sfe) <- c("tri2nb", "visium")

# MARGIN = 1 means rowGraphs; MARGIN = 3 means annotation graphs (annotGraphs)
# for both getters and setters

# Set single graph by
# Spatial graph for myofibers
g_myofiber <- findSpatialNeighbors(sfe,
    type = "myofiber_simplified",
    MARGIN = 3L
)
spatialGraph(sfe, type = "myofiber", MARGIN = 3L) <- g_myofiber
# Or equivalently
annotGraph(sfe, "myofiber") <- g_myofiber

# Get a specific graph by name
g <- spatialGraph(sfe, "myofiber", MARGIN = 3L)
g2 <- spatialGraph(sfe, "visium", MARGIN = 2L)
# Or equivalently
g <- annotGraph(sfe, "myofiber")
g2 <- colGraph(sfe, "visium")