Get parameters used in spatial methods

The getParams function allows users to access the parameters used to compute the results that may be stored in colFeatureData.

Usage

getParams(
  sfe,
  name,
  local = FALSE,
  colData = FALSE,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  reducedDimName = NULL
)

Arguments

sfe

A SpatialFeatureExperiment object.

name

Name used to store the results.

local

Logical, whether the results of interest come from a local spatial method.

colData

Logical, whether the results were computed for a column of colData(sfe).

colGeometryName

To get results for a colGeometry.

annotGeometryName

To get results for an annotGeometry; colGeometry has precedence so this argument is ignored if colGeometryName is specified.

reducedDimName

Name of a dimension reduction, can be seen in reducedDimNames. colGeometryName and annotGeometryName have precedence over reducedDimName.

Value

A named list showing the parameters

Examples

library(SFEData)
library(scater)
#> Loading required package: scuttle
#> Loading required package: ggplot2
#> 
#> Attaching package: ‘ggplot2’
#> The following object is masked from ‘package:SpatialFeatureExperiment’:
#> 
#>     unit
library(Voyager)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
sfe <- colDataMoransI(sfe, "nCounts")
getParams(sfe, "moran", colData = TRUE)
#> $name
#> [1] "moran"
#> 
#> $package
#> [1] "spdep"
#> 
#> $version
#> [1] ‘1.3.3’
#> 
#> $zero.policy
#> NULL
#> 
#> $include_self
#> [1] FALSE
#> 
#> $graph_params
#> $graph_params$FUN
#> [1] "findVisiumGraph"
#> 
#> $graph_params$package
#> $graph_params$package[[1]]
#> [1] "SpatialFeatureExperiment"
#> 
#> $graph_params$package[[2]]
#> [1] ‘1.6.1’
#> 
#> 
#> $graph_params$args
#> $graph_params$args$style
#> [1] "W"
#> 
#> $graph_params$args$zero.policy
#> NULL
#> 
#> $graph_params$args$sample_id
#> [1] "Vis5A"
#> 
#> 
#>