binAcrossPixels {imcRtools} | R Documentation

## 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 (nils.eling@dqbm.uzh.ch)

### 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)

[Package imcRtools version 1.0.2 Index]