Get global spatial analysis results and metadata of colData, rowData, and geometries
Source:R/featureData.R
colFeatureData.Rd
Results of spatial analyses on columns in colData
, rowData
, and
geometries are stored in their metadata. 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
.
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