removeEmptySpace: Remove empty space

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

Remove empty space

Description

For each sample independently, all geometries and spatialCoords are translated so the origin is at the minimum coordinates of the bounding box of all geometries of the sample. This way coordinates of different samples will be more comparable. This removes empty space in the images if present.

Usage

removeEmptySpace(sfe, sample_id = "all")

Arguments

sfe	An SFE object.
sample_id	Sample to remove empty space.

Value

An SFE object with empty space removed.

Note

Unlike other functions in this package, this function operates on all samples by default.

Examples

library(SFEData)
library(SingleCellExperiment)
sfe <- McKellarMuscleData("full")
# Only keep spots on tissue
sfe <- sfe[, colData(sfe)$in_tissue]
# Move the coordinates of the tissue
sfe <- removeEmptySpace(sfe)

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.