binAcrossPixels: Aggregate consecutive pixels per single-metal spot

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

Aggregate consecutive pixels per single-metal spot

Description

Helper function for estimating the spillover matrix. Per metal spot, consecutive pixels a aggregated (default: summed).

Usage

binAcrossPixels(
  object,
  bin_size,
  spot_id = "sample_id",
  assay_type = "counts",
  statistic = "sum",
  ...
)

Arguments

object	a SingleCellExperiment object containing pixel intensities for all channels. Individual pixels are stored as columns and channels are stored as rows.
bin_size	single numeric indicating how many consecutive pixels per spot should be aggregated.
spot_id	character string indicating which colData(object) entry stores the isotope names of the spotted metal.
assay_type	character string indicating which assay to use.
statistic	character string indicating the statistic to use for aggregating consecutive pixels.
...	additional arguments passed to aggregateAcrossCells

Value

returns the binned pixel intensities in form of a SingleCellExperiment object

Author(s)

Nils Eling ([e-mail])

See Also

aggregateAcrossCells for the aggregation function

Examples

path <- system.file("extdata/spillover", package = "imcRtools")
# Read in .txt files
sce <- readSCEfromTXT(path)
dim(sce)

# Visualizes heatmap before aggregation
plotSpotHeatmap(sce)

# Sum consecutive pixels
sce <- binAcrossPixels(sce, bin_size = 10)
dim(sce)

# Visualizes heatmap after aggregation
plotSpotHeatmap(sce)

BodenmillerGroup/imcRtools documentation built on Oct. 30, 2024, 12:19 p.m.