R/PlateLayoutFunctions.R

In jakeyeung/scchic-functions:

# Jake Yeung
# Date of Creation: 2020-09-13
# File: ~/projects/scchic-functions/R/PlateLayoutFunctions.R
#



GetPlateWellFromRowCol <- function(jrow, jcol){
  # convert row (1 to 16 to A to P) to get A1 or A2 etc
  # assertthat::assert_that(is.integer(jrow))
  # assertthat::assert_that(is.integer(jcol))
  rowletter <- toupper(letters)[jrow]
  wellname <- paste0(rowletter, jcol)
  return(wellname)
}



IsRound1 <- function(samp, mark = "H3K4me1"){
  if (mark == "H3K4me1"){
    wt.plates <- c("B6-13W1-BM-H3K4me1", "PZ-ChIC-Bl6-BM-H3K4me1-Index")
    linneg.plates <- c("PZ-ChIC-Bl6-BM-lin-H3K4me1-")
    hsc.plates <- c("-stem-cells-")
  } else if (mark == "H3K4me3"){
    wt.plates <- c("B6-13W1-BM-H3K4me3")
    linneg.plates <- c("-Linneg-")
    hsc.plates <- c("-B6BMSC-")
  } else if (mark == "H3K27me3") {
    wt.plates <- c("B6-13W1-BM-")
    linneg.plates <- c("-Linneg-")
    hsc.plates <- c("-B6BMSC-")
  } else if (mark == "H3K9me3") {
    wt.plates <- c("B6-13W1-BM-")
    linneg.plates <- c("-Linneg-")
    hsc.plates <- c("BMSC-")
  } else {
    print(paste(mark, "not yet coded"))
  }
  wt.plates.grep <- paste(wt.plates, collapse = "|")
  linneg.plates.grep <- paste(linneg.plates, collapse = "|")
  hsc.plates.grep <- paste(hsc.plates, collapse = "|")
  is.wt <- grepl(wt.plates.grep, samp)
  is.linneg <- grepl(linneg.plates.grep, samp)
  is.hsc <- grepl(hsc.plates.grep, samp)
  bool.vec <- c(is.wt, is.linneg, is.hsc)
  # print(bool.vec)
  if (all(!bool.vec)){
    return("Round2")
  }
  indx <- which.max(bool.vec)
  if (indx == 1){
    cond <- "Unenriched"
  } else if (indx == 2){
    cond <- "Linneg"
  } else if (indx == 3){
    cond <- "StemCell"
  } else {
    print(paste("Unexpected indx should be 1, 2, 3:", cond))
  }
}


SplitGetLast <- function(x, jsplit = "-"){
  # get last element after splitting
  xsplit <- strsplit(x, jsplit)[[1]]
  xnew <- xsplit[[length(xsplit)]]
  return(xnew)
}

GetRepBM <- function(experiname){
  if (grepl("rep3", experiname)){
    return("rep3")
  } else if (grepl("rep2", experiname)){
    return("rep2")
  } else {
    print("Neither rep2 nor rep3 in name: Returning rep3")
    return("rep3")
  }
}


AnnotateSortFromLayout.dat <- function(jdat){
  # expects cell in colname
  jdat <- bind_rows(jdat) %>%
    rowwise() %>%
    mutate(experi = ClipLast(cell, jsep = "_"),
           plate = as.numeric(strsplit(experi, "-")[[1]][[6]]),
           rowcoord = AddPlateCoordinates(cell)$rowcoord,
           colcoord = AddPlateCoordinates(cell)$colcoord,
           stype = AnnotateSortFromLayout(plate, rowcoord, colcoord))
  return(jdat)
}



AnnotateSortFromLayoutBMall <- function(plate, rowcoord, colcoord, jrep, jmark){
  assertthat::assert_that(is.numeric(plate))
  assertthat::assert_that(is.numeric(rowcoord))
  assertthat::assert_that(is.numeric(colcoord))
  # assertthat::assert_that(is.numeric(jrep))

  if (jrep == "rep3"){
    ctype <- AnnotateSortFromLayout(plate = plate, rowcoord = rowcoord, colcoord = colcoord)
  } else if (jrep == "rep2"){
    ctype <- AnnotateSortFromLayout.rep2(plate = plate, rowcoord = rowcoord, colcoord = colcoord, jmark = jmark)
  }
  return(ctype)
}



AnnotateSortFromLayout.rep2 <- function(plate, rowcoord, colcoord, jmark){
  assertthat::assert_that(is.numeric(plate))
  assertthat::assert_that(is.numeric(rowcoord))
  assertthat::assert_that(is.numeric(colcoord))
  if (rowcoord >= 1 & rowcoord <= 8 & colcoord == 1){
    print("Empty cell")
    warning("Empty cell")
    ctype <- "Empty"
    return(ctype)
  }
  if ( (plate == 1 | plate == 2) & jmark == "H3K4me1" ){
    if (colcoord >= 1 & colcoord <= 11){
      ctype <- "Unenriched"
    } else if (colcoord >= 12 & colcoord <= 18){
      ctype <- "LinNeg"
    } else if (colcoord >= 19 & colcoord <= 24){
      ctype <- "LSK"
    }
  } else {
    if (colcoord >= 1 & colcoord <= 11){
        ctype <- "Unenriched"
      } else if (colcoord >= 12 & colcoord <= 19){
        ctype <- "LinNeg"
      } else if (colcoord >= 20 & colcoord <= 24){
        ctype <- "LSK"
      }
  }
  # } else if (plate >= 3 & plate <= 6) {
  #   if (colcoord >= 1 & colcoord <= 11){
  #     ctype <- "Unenriched"
  #   } else if (colcoord >= 12 & colcoord <= 19){
  #     ctype <- "LinNeg"
  #   } else if (colcoord >= 20 & colcoord <= 24){
  #     ctype <- "LSK"
  #   }
  # } else {
  #   print(paste("Unknown plate:", plate))
  #   ctype <- "Unknown"
  # }
  return(ctype)
}




AnnotateSortFromLayout <- function(plate, rowcoord, colcoord){
  assertthat::assert_that(is.numeric(plate))
  assertthat::assert_that(is.numeric(rowcoord))
  assertthat::assert_that(is.numeric(colcoord))
  if (rowcoord >= 1 & rowcoord <= 8 & colcoord == 1){
    print("Empty cell")
    warning("Empty cell")
    ctype <- "Empty"
    return(ctype)
  }
  if (plate >= 1 & plate <= 7){
    if (colcoord >= 1 & colcoord <= 11){
      ctype <- "Unenriched"
    } else if (colcoord >= 12 & colcoord <= 18){
      ctype <- "LinNeg"
    } else if (colcoord >= 19 & colcoord <= 24){
      ctype <- "LSK"
    }

  } else if (plate >= 8 & plate <= 13){
    if (colcoord >= 1 & colcoord <= 12){
      ctype <- "Unenriched"
    } else if (colcoord >= 13 & colcoord <= 24){
      ctype <- "LinNeg"
    }
  } else {
    print(paste("Unknown plate:", plate))
    ctype <- "Unknown"
  }
  return(ctype)
}