R/flareFunc.R

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# flareFunc: Calculate the weighted mean of a square to detect plate flares
#-------------------------------------------------------------------------------

#' @title Calculate the weighted mean of a square to detect plate flares
#'
#' @description
#' \code{flareFunc} calculates the weighted mean of square regions to detect
#' plate flares.
#'
#' @param val Numeric, the well values
#' @param coli Integer, the well column index
#' @param rowi Integer, the well row index
#' @param apid Character, the assay plate id
#' @param r Integer, the number of wells from the center well (in one
#' direction) to make the square
#'
#' @seealso \code{\link{MC6_Methods}}, \code{\link{Method functions}},
#' \code{\link{mc6}}
#' 
#' @keywords internal
#' 
#' @return None
#' 
#' @import data.table
#' @importFrom stats dist

flareFunc <- function(val, coli, rowi, apid, r){

    ## Variable-binding to pass R CMD Check
    cold <- rowd <- flrv <- index <- NULL

    if (r > 4) r <- 4
    nrep <- (1 + 2*r)^2
    minc <- min(coli)
    maxc <- max(coli)
    minr <- min(rowi)
    maxr <- max(rowi)
    ordr <- order(apid, coli, rowi)
    val  <- val[ordr]
    val[val > 100] <- 100
    coli <- coli[ordr]
    rowi <- rowi[ordr]
    apid <- apid[ordr]
    val_len <- length(val)
    adj     <- -r:r
    adj     <- c(0, adj[-which(adj == 0)])
    adj_len <- length(adj)
    adjc <- rep(adj, each=adj_len)
    adjr <- rep(adj, times= adj_len)
    adjd <- 1/as.matrix(dist(cbind(adjc, adjr)))[ , 1]
    adjd[1] <- 1
    dat <- data.table(
        val=rep(val, nrep),
        coli=rep(coli, nrep),
        rowi=rep(rowi, nrep),
        apid=rep(apid, nrep),
        ordr=rep(ordr, nrep),
        index=rep(seq_len(nrep), each=val_len),
        cold=rep(adjc, each=val_len),
        rowd=rep(adjr, each=val_len),
        adjd=rep(adjd, each=val_len)
    )
    
    dat[, coli := coli + cold]
    dat[, rowi := rowi + rowd]
    dat[, flrv := sum(
            val*adjd, na.rm=TRUE
        )/nrep - max(val*adjd, na.rm=TRUE)/nrep,
        by=list(apid, coli, rowi)]
    dat[index == 1, flrv][order(ordr)][]

}

#-------------------------------------------------------------------------------