Reduce a high resolution image measurement (origin) to a lower resolution measurement (target)

Source: R/spat_reduce.R

spat_reduce() Creates a single SpatialExperiment object with all measurements mapped to the same coordinate space for plotting and analysis

spat_reduce(
  spe_target,
  spe_origin,
  origin_assay = "lipids",
  target_dims = c("spot_width", "spot_height"),
  replace_nas = FALSE,
  stat = "mean"
)

Arguments

spe_target

Low resolution image measurements

spe_origin

High-resolution image measurements to be mapped to target

origin_assay

Name of assay in origin assay to be reduced

target_dims

Names of width and height of target spots, respectively

replace_nas

Set to TRUE if we want to replace NA values with zeroes. This will increase the number of data points in common for correlation calculations.

stat

Statistic used to summarize regions, choices are currently 'mean' and 'median'

Value

A copy of the spe_target object with the altExp slot containing a reduced version of the origin

Details

This function allows us to map two distinct omics measurements to the same coordinate system. It takes on 'origin' measurement and summarizes the values (typically via mean) in the ROI in a 'target' measurement so that the source and target values can be compared.