Aggregate consecutive pixels per single-metal spot

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

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

See also

aggregateAcrossCells for the aggregation function

Author

Nils Eling (nils.eling@dqbm.uzh.ch)

Examples

path <- system.file("extdata/spillover", package = "imcRtools")
# Read in .txt files
sce <- readSCEfromTXT(path)
#> Spotted channels:  Dy161, Dy162, Dy163, Dy164
#> Acquired channels:  Dy161, Dy162, Dy163, Dy164
#> Channels spotted but not acquired:  
#> Channels acquired but not spotted:  
dim(sce)
#> [1]   4 400

# Visualizes heatmap before aggregation
plotSpotHeatmap(sce)


# Sum consecutive pixels
sce <- binAcrossPixels(sce, bin_size = 10)
dim(sce)
#> [1]  4 40

# Visualizes heatmap after aggregation
plotSpotHeatmap(sce)