spatialGraphs: Spatial graph methods

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Spatial graph methods

Description

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.

Usage

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

## S4 replacement method for signature '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 signature '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 replacement method for signature '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")
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")
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")
# Or equivalently (sample_id optional as only one sample is present)
colGraphNames(sfe)

# 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")

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.