Get global spatial analysis results and metadata of colData, rowData, and geometries

Results of spatial analyses on columns in colData, rowData, and geometries are stored in their metadata, which can be accessed by the metadata function. The colFeaturedata function allows the users to more directly access these results.

Usage

colFeatureData(sfe)

rowFeatureData(sfe)

geometryFeatureData(sfe, type, MARGIN = 2L)

reducedDimFeatureData(sfe, dimred)

Arguments

sfe

An SFE object.

type

Which geometry, can be name (character) or index (integer)

MARGIN

Integer, 1 means rowGeometry, 2 means colGeometry, and 3 means annotGeometry. Defaults to 2, colGeometry.

dimred

Name of a dimension reduction, can be seen in reducedDimNames.

Value

A DataFrame.

See also

getParams

Examples

library(SpatialFeatureExperiment)
library(SingleCellExperiment)
library(SFEData)
library(Voyager)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
# Moran's I for colData
sfe <- colDataMoransI(sfe, "nCounts")
colFeatureData(sfe)
#> DataFrame with 12 rows and 2 columns
#>           moran_Vis5A   K_Vis5A
#>             <numeric> <numeric>
#> barcode            NA        NA
#> col                NA        NA
#> row                NA        NA
#> x                  NA        NA
#> y                  NA        NA
#> ...               ...       ...
#> sample_id          NA        NA
#> nCounts      0.675416   1.67027
#> nGenes             NA        NA
#> prop_mito          NA        NA
#> in_tissue          NA        NA