colFeatureData: Get global spatial analysis results and metadata of colData,...

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

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

Description

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")
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
# Moran's I for colData
sfe <- colDataMoransI(sfe, "nCounts")
colFeatureData(sfe)

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.