#
# Authors: Florent Chuffart, INSERM and Magali Richard, CNRS
# florent.chuffart@univ-grenoble-alpes.fr
# mag.richard@ens-lyon.fr
#
#---------------------------------------------
#' Export final data
#'
#' This function works on FL1H, FSC and SSC data acquired on 96-well plates
#' @param data The data to be exported
#' @return A data tab
#' @export
export_data = function (data ){
meanFL1lin = NULL
varFL1lin = NULL
meanFL1log = NULL
varFL1log = NULL
on_frac = NULL
ncells = NULL
meanFSC = NULL
meanSSC = NULL
on_thresholdlin = NULL
on_thresholdlog = NULL
for (i in 1:dim(data$anno)[1]){
print(i)
cur = data$ngdat
linfl1 = 10^(4 * cur[[i]]$FL1.H / 1024) * 1
on_thresholdlin[i] = 10^(4 * data$anno$on_threshold[i] / 1024) * 1
on_thresholdlog[i] = data$anno$on_threshold[i]
on_frac[i] = data$anno$on_frac[i]
meanFL1lin[i] = mean(linfl1)
meanFL1log[i] = mean(cur[[i]]$FL1.H)
varFL1lin[i] = var(linfl1)
varFL1log[i] = var(cur[[i]]$FL1.H)
ncells[i] = dim(cur[[i]])[1]
meanFSC[i] = mean(cur[[i]]$FSC.H)
meanSSC[i] = mean(cur[[i]]$SSC.H)
}
export <- cbind(data$anno[,c("date","time", "gal", "strain", "bg")], meanFL1lin, varFL1lin, on_frac, on_thresholdlin, meanFL1log, varFL1log, on_frac, on_thresholdlog, ncells, meanFSC, meanSSC)
date=unique(data$anno$date)
write.table(export, file = paste("outputs/",date,"_gal3_priors.tab", sep = ""), quote = FALSE, row.names=FALSE)
return(export)
}
# export_data = function (data){
# meanFL1 = NULL
# varFL1 = NULL
# ncells = NULL
# meanFSC = NULL
# meanSSC = NULL
# nb_on = NULL
# nb_off = NULL
# fraction_on = NULL
# for (i in 1:dim(data$anno)[1]){
# cur = data$ngdat
# linfl1 = 10^(4 * cur[[i]]$FL1.H / 1024) * 1
# meanFL1[i] = mean(linfl1)
# varFL1[i] = var(linfl1)
# ncells[i] = dim(cur[[i]])[1]
# meanFSC[i] = mean(cur[[i]]$FSC.H)
# meanSSC[i] = mean(cur[[i]]$SSC.H)
# nb_on[i] = data$anno$nb_on[i]
# nb_off[i] = data$anno$nb_off[i]
# fraction_on[i] = data$anno$fraction_on[i]
# }
# export <- cbind(data$anno[,c("date","time", "gal", "strain", "bg")], meanFL1, varFL1, nb_on, nb_off, fraction_on, ncells, meanFSC, meanSSC)
# date=unique(data$anno$date)
# write.table(export, file = paste("outputs/",date,"_gal3_priors.tab", sep = ""), quote = FALSE, row.names=FALSE)
# return(export)
# }
# export_data = function (data, type="norm" ){
# meanFL1 = NULL
# varFL1 = NULL
# on_frac = NULL
# ncells = NULL
# meanFSC = NULL
# meanSSC = NULL
# on_threshold = NULL
# for (i in 1:dim(data$anno)[1]){
# cur = data$ngdat
# if (type=="norm") {
# cur = data$ngdat
# on_threshold[i] = 10^(4 * data$anno$on_threshold[i] / 1024) * 1
# on_frac[i] = data$anno$ngon_frac[i]
# } else if (type=="not_norm") {
# cur = data$gdat
# on_threshold[i] = 10^(4 * data$anno$on_threshold[i] / 1024) * 1
# on_frac[i] = data$anno$gon_frac[i]
# }
# linfl1 = 10^(4 * cur[[i]]$FL1.H / 1024) * 1
# meanFL1[i] = mean(linfl1)
# varFL1[i] = var(linfl1)
# ncells[i] = dim(cur[[i]])[1]
# meanFSC[i] = mean(cur[[i]]$FSC.H)
# meanSSC[i] = mean(cur[[i]]$SSC.H)
# }
# export <- cbind(data$anno[,c("date","time", "gal", "strain", "bg")], meanFL1, varFL1, on_frac, on_threshold, ncells, meanFSC, meanSSC)
# date=unique(data$anno$date)
# write.table(export, file = paste("outputs/",date,"_gal3_priors.tab", sep = ""), quote = FALSE, row.names=FALSE)
# return(export)
# }
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