colFeatureData: Get global spatial analysis results and metadata of colData,...
In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf
colFeatureData R Documentation
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. 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 Dec. 20, 2024, 3:41 a.m.
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| colFeatureData | R Documentation |
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. 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
|
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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