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, 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
.
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