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 ifcolGeometryName
is specified.- reducedDimName
Name of a dimension reduction, can be seen in
reducedDimNames
.colGeometryName
andannotGeometryName
have precedence overreducedDimName
.
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] ‘1.3.6’
#>
#> $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] "1.8.2"
#>
#>
#> $graph_params$args
#> $graph_params$args$style
#> [1] "W"
#>
#> $graph_params$args$zero.policy
#> NULL
#>
#> $graph_params$args$sample_id
#> [1] "Vis5A"
#>
#>
#>