binAcrossPixels {imcRtools} | R Documentation |
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", ... )
object |
a |
bin_size |
single numeric indicating how many consecutive pixels per spot should be aggregated. |
spot_id |
character string indicating which |
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 |
returns the binned pixel intensities in form of a
SingleCellExperiment
object
Nils Eling (nils.eling@dqbm.uzh.ch)
aggregateAcrossCells
for the aggregation
function
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)