localResults: Organize results from local spatial statistics

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

Organize results from local spatial statistics

Description

Local spatial statics like local Moran's I, local Geary's C, Getis-Ord Gi*, and geographically weighted summary statistics return values at each spatial location. Just like dimension reductions, these results are clearly associated with the broader SFE object, so they should have a place within the object. However, a separate field is needed because these analyses are conceptually distinct from dimension reduction. Also, each feature (e.g. gene) can have its own results with values at each location. The localResults field in the SFE object stores these results that has a value for each spatial location.

Usage

## S4 method for signature 'SpatialFeatureExperiment,missing,missing'
localResults(
  x,
  sample_id = NULL,
  name,
  features = NULL,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  withDimnames = TRUE,
  ...
)

## S4 replacement method for signature 'SpatialFeatureExperiment,missing,missing'
localResults(
  x,
  sample_id = NULL,
  name,
  features = NULL,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  withDimnames = TRUE,
  ...
) <- value

## S4 method for signature 'SpatialFeatureExperiment,ANY,character'
localResults(
  x,
  sample_id = NULL,
  name,
  features = NULL,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  withDimnames = TRUE,
  swap_rownames = NULL,
  ...
)

## S4 replacement method for signature 'SpatialFeatureExperiment,ANY,character'
localResults(
  x,
  sample_id = NULL,
  name,
  features = NULL,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  withDimnames = TRUE,
  ...
) <- value

## S4 method for signature 'SpatialFeatureExperiment'
localResultNames(x)

## S4 replacement method for signature 'SpatialFeatureExperiment,character'
localResultNames(x) <- value

## S4 method for signature 'SpatialFeatureExperiment'
localResultFeatures(
  x,
  type = 1L,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  swap_rownames = NULL
)

## S4 method for signature 'SpatialFeatureExperiment'
localResultAttrs(
  x,
  type = 1L,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  swap_rownames = NULL
)

## S4 method for signature 'SpatialFeatureExperiment,missing'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE,
  simplify = TRUE,
  swap_rownames = NULL
)

## S4 method for signature 'SpatialFeatureExperiment,numeric'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE,
  simplify = TRUE,
  swap_rownames = NULL
)

## S4 method for signature 'SpatialFeatureExperiment,character'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE,
  simplify = TRUE,
  swap_rownames = NULL
)

## S4 replacement method for signature 'SpatialFeatureExperiment,missing'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE
) <- value

## S4 replacement method for signature 'SpatialFeatureExperiment,numeric'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE
) <- value

## S4 replacement method for signature 'SpatialFeatureExperiment,character'
localResult(
  x,
  type,
  feature,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  sample_id = NULL,
  withDimnames = TRUE
) <- value

Arguments

x	A SpatialFeatureExperiment object.
sample_id	Sample ID to get or set geometries.
name	Name of the spatial method used, such as "localmoran".
features	Features whose local results to get or set, for localResults getter and setter for multiple features at a time.
colGeometryName	Which colGeometry to get or set local results.
annotGeometryName	Which annotGeometry to get or set local results.
withDimnames	Logical. If TRUE, then the dimnames (colnames or rownames) of the gene count matrix should correspond to row names of the sf data frames of interest.
...	Ignored
value	Values to set, should be either a matrix or a data frame.
swap_rownames	Name of a column in rowData to identify features instead of the row names of the SFE object. For example, if the row names of the SFE object are Ensembl IDs and gene symbols are in the "symbol" column in rowData, then putting "symbol" for this argument will use the gene symbols to identify which gene's local results to get or set.
type	Name or index of the spatial method used, such as "localmoran".
feature	Feature whose local results to get or set, for localResult getter and setter for one feature at a time.
simplify	Basically whether to return the content of the list rather than a list when the list only has one element, such as results for one type and one feature.

Value

localResults returns a named list each element of which is a set of local results of interest. localResult returns a matrix or a data frame, whichever the original is when it's set. localResultNames returns a character vector. Setters return an SFE object with the desired field set. For genes and colData columns, the local results are stored in the localResults field in int_colData, whereas for colGeometries and annotGeometries, the local results are stored as columns in the same sf data frames. localResultFeatures returns a character vector of names of features for which local results are available. localResultAttrs returns a character vector of the column names of the local results of one type for one feature. It returns NULL if the results are a vector.

Examples

# Toy example
sfe <- readRDS(system.file("extdata/sfe_toy.rds",
    package = "SpatialFeatureExperiment"
))
# localResults functions are written for organizing results from local
# spatial statistics (see the Voyager package). But for the examples here,
# random toy matrices are used. The real results are often matrices, with a
# matrix for each feature.
library(S4Vectors)
set.seed(29)
toy_res1 <- matrix(rnorm(10),
    nrow = 5, ncol = 2,
    dimnames = list(colnames(sfe), c("meow", "purr"))
)
toy_res1b <- matrix(rgamma(10, shape = 2),
    nrow = 5, ncol = 2,
    dimnames = list(colnames(sfe), c("meow", "purr"))
)
toy_df1 <- DataFrame(gene1 = I(toy_res1), gene2 = I(toy_res1b))

toy_res2 <- matrix(rpois(10, lambda = 2),
    nrow = 5, ncol = 2,
    dimnames = list(colnames(sfe), c("sassy", "tortitude"))
)
toy_df2 <- DataFrame(gene1 = I(toy_res2))
# Set all local results
localResults(sfe) <- list(localmoran = toy_df1, Gistar = toy_df2)
# Get all local results
lrs <- localResults(sfe)

# Set results of the same type for multiple genes
localResults(sfe, name = "localmoran") <- toy_df1
# Can also use a list
localResults(sfe, name = "localmoran") <- as.list(toy_df1)
# Get results of the same type for multiple genes
lrs <- localResults(sfe, name = "localmoran", features = c("gene1", "gene2"))

# Set results for one type and one gene
localResult(sfe, "localmoran", feature = "gene1") <- toy_res1
# Get results for one type and one gene
lr <- localResult(sfe, "localmoran", feature = "gene1")

# Set results for a feature in colGeometries
cg_toy <- readRDS(system.file("extdata/cg_toy.rds",
    package = "SpatialFeatureExperiment"
))
colGeometry(sfe, "cg") <- cg_toy
localResult(sfe, "localmoran",
    feature = "gene1",
    colGeometryName = "cg"
) <- toy_res1
# Get results for a feature in colGeometries
lr <- localResult(sfe, "localmoran", "gene1", colGeometryName = "cg")

pachterlab/SpatialFeatureExperiment documentation built on March 11, 2024, 11:11 p.m.