Deprecated/MULTI-seq.Utils.R

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

# _________________________________________________________________________________________________
# MULTI-seq.Utils.R ______________________________ ----
# _________________________________________________________________________________________________
# source('~/GitHub/Packages/Seurat.utils/R/MULTI-seq.Utils.R')
# try(source('https://raw.githubusercontent.com/vertesy/Seurat.utils/master/Functions/MULTI-seq.functions.R'))

# Requirements __________________________________________
# try(require(MarkdownReports),  silent = T)
# try(require(pheatmap),  silent = T)
# May also require


# _________________________________________________________________________________________________
#' @title BarTableSweepList
#'
#' @description Generate a list of classified cells for a range of quantiles.
#' @param min The minimum quantile value. Default: 0.01.
#' @param max The maximum quantile value. Default: 0.99.
#' @param step The step size to increment the quantile. Default: 0.02.
#' @param bar_table The barcode table to be used. Default: bar.table.
#' @return A list of classified cells for each quantile in the specified range.
#' @examples
#' \dontrun{
#' if (interactive()) {
#'   bar.table_sweep.list <- BarTableSweepList(bar_table = bar.table.solo) # Quantile Sweep List
#' }
#' }
#' @export
BarTableSweepList <- function(min = 0.01, max = 0.99, step = 0.02, bar_table = bar.table) {
  bar.table_sweep.list <- list()
  n <- 0
  Quantiles <- seq(from = min, to = max, by = step)
  for (n in 1:length(Quantiles)) { # print(q)
    bar.table_sweep.list[[n]] <- classifyCells(bar_table, q = Quantiles[n])
    names(bar.table_sweep.list)[n] <- paste("q=", Quantiles[n], sep = "")
  }
  return(bar.table_sweep.list)
}





# _________________________________________________________________________________________________
#' @title mSeq.map.all96.BCs
#'
#' @description Map all 96 barcode sequences.
#' @param readTable The table of read counts. Default: readTable.
#' @param CellIDs The identifiers for the cells. Default: CellIDs.
#' @param path2allBCs The path to the reference barcode sequences file. Default: '~/Google_Drive/Science/IMBA/MULTI.seq/from.US/All.MULTI-seq_barcodes.Mar2019.tsv'.
#' @return The mapped barcode sequences.
#' @examples
#' \dontrun{
#' if (interactive()) {
#'   bar.table <- mSeq.map.all96.BCs(readTable = readTable, CellIDs = CellIDs)
#' }
#' }
#' @export
mSeq.map.all96.BCs <- function(
    readTable = readTable, CellIDs = CellIDs,
    path2allBCs = "~/Google_Drive/Science/IMBA/MULTI.seq/from.US/All.MULTI-seq_barcodes.Mar2019.tsv") {
  (bar.ref <- read_tsv(path2allBCs)[[1]]) # Vector of reference all MULTI-seq sample barcode sequences.
  MULTIseq.align(readTable = readTable, cellIDs = CellIDs, ref = bar.ref)
}



# _________________________________________________________________________________________________

#' @title aux_plotAllMseqBCs
#'
#' @description Plot all MULTI-seq barcodes.
#' @param bar.table The barcode table to be used. Default: bar.table[,1:96].
#' @param barcodes.used The barcodes that have been used. Default: BCs.used.
#' @param plotname The title of the plot. Default: 'Barcode seq depth'.
#' @return A plot of all MULTI-seq barcodes.
#' @examples
#' \dontrun{
#' if (interactive()) {
#'   aux_plotAllMseqBCs(bar.table = bar.table[, 1:96], barcodes.used = BCs.used, plotname = "Barcode seq depth")
#' }
#' }
#' @export
aux_plotAllMseqBCs <- function(
    bar.table = bar.table[, 1:96], barcodes.used = BCs.used,
    plotname = "Barcode seq depth") {
  stopifnot(is.numeric(BCs.used))
  BC.depth <- colSums(bar.table)[1:96]
  if (min(BC.depth) < 1) {
    BC.depth <- BC.depth + 1
  }
  log.depth <- log10(BC.depth)
  range(log.depth)
  ccc <- colnames(bar.table) %in% BCs.used

  wbarplot(log.depth,
    col = ccc, lwd = 1, lcol = 1, lty = 2, plotname = plotname,
    vline = (range(BCs.used) + c(-1, 1)),
    hline = quantile(log.depth[setdiff(1:69, BCs.used)], .95),
    ylab = "log10(total reads / BC)", main = plotname
  )
  wlegend.label(
    "    Horiz. line at 95%
    of unused BC's.
    Vertical line: range
    of used BCs.",
    poz = 2, cex = 1
  )
}


# _________________________________________________________________________________________________
# bar.table.log <- t(log10(bar.table[,BCs.used]+1))
# bar.table.log <- CodeAndRoll2::clip.outliers.at.percentile(bar.table.log)