R/do.calculate.area.R

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

#' do.calculate.area
#'
#' @param dat NO DEFAULT. Spatial data list
#' @param region DEFAULT = NULL. Name of the region mask, if present.
#'
#' @import data.table
#'
#' @export

do.calculate.area <- function(dat,
                              region = NULL){
  
  ### Setup
  
      # dat <- spatial.dat
      # region <- 'regions'
  
  ### Preparation
  
    roi.names <- names(dat)
  
  ### Processing
  
      area.list <- list()
      
      for(i in roi.names){
        
        # i <- roi.names[[1]]
    
        ## If region masks are present
        
            if(!is.null(region)){
              
              poly.names <- dat[[i]]@MASKS[[region]]$polygons@data
              
              areas <- area(dat[[i]]@MASKS[[region]]$polygons)
              areas <- sqrt(areas)
              areas <- as.data.table(t(areas))
              
              names(areas) <- as.character(poly.names[[1]])
              
              # total.area <- sqrt(dim(dat[[i]]$RASTERS[[1]])[1] * dim(dat[[i]]$RASTERS[[1]])[2])
              # total.area <- as.data.table(total.area)
              # names(total.area) <- 'Total'
              # areas <- cbind(areas, total.area)
              area.list[[i]] <- areas
              
            }
        
        ## If region masks are NOT present
            if(is.null(region)){
              
              total.area <- sqrt(dim(dat[[i]]@RASTERS[[1]])[1] * dim(dat[[i]]@RASTERS[[1]])[2])
              total.area <- as.data.table(total.area)
              
              names(total.area) <- 'Total'
              area.list[[i]] <- total.area
              
            }
      }
      
      area.list
      
      area.res <- rbindlist(area.list, fill = TRUE)
      area.res <- cbind(roi.names, area.res)
      names(area.res)[1] <- "ROI"
      
  ### Return
  
  return(area.res)
  
}