R/wetlab.R

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

#' making a 96-well plate index
#'
#' @return named vector (Well --> location); column-wise location
.well96_index = function(){
  wells = c('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1',
            'A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2',
            'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3',
            'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4',
            'A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5',
            'A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6',
            'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7',
            'A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8',
            'A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9',
            'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10',
            'A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11',
            'A12', 'B12', 'C12', 'D12', 'E12', 'F12', 'G12', 'H12')
  idx = 1:length(wells)
  names(idx) = wells
  return(idx)
}

#' making 384-well plate index
#'
#' @return named vector (Well --> location); column-wise location
.well384_index = function(){
  wells = c('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1', 'I1', 'J1', 'K1', 'L1', 'M1', 'N1', 'O1', 'P1',
            'A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2', 'I2', 'J2', 'K2', 'L2', 'M2', 'N2', 'O2', 'P2',
            'A3', 'B3', 'C3', 'D3', 'E3', 'F3', 'G3', 'H3', 'I3', 'J3', 'K3', 'L3', 'M3', 'N3', 'O3', 'P3',
            'A4', 'B4', 'C4', 'D4', 'E4', 'F4', 'G4', 'H4', 'I4', 'J4', 'K4', 'L4', 'M4', 'N4', 'O4', 'P4',
            'A5', 'B5', 'C5', 'D5', 'E5', 'F5', 'G5', 'H5', 'I5', 'J5', 'K5', 'L5', 'M5', 'N5', 'O5', 'P5',
            'A6', 'B6', 'C6', 'D6', 'E6', 'F6', 'G6', 'H6', 'I6', 'J6', 'K6', 'L6', 'M6', 'N6', 'O6', 'P6',
            'A7', 'B7', 'C7', 'D7', 'E7', 'F7', 'G7', 'H7', 'I7', 'J7', 'K7', 'L7', 'M7', 'N7', 'O7', 'P7',
            'A8', 'B8', 'C8', 'D8', 'E8', 'F8', 'G8', 'H8', 'I8', 'J8', 'K8', 'L8', 'M8', 'N8', 'O8', 'P8',
            'A9', 'B9', 'C9', 'D9', 'E9', 'F9', 'G9', 'H9', 'I9', 'J9', 'K9', 'L9', 'M9', 'N9', 'O9', 'P9',
            'A10', 'B10', 'C10', 'D10', 'E10', 'F10', 'G10', 'H10', 'I10', 'J10', 'K10', 'L10', 'M10', 'N10', 'O10', 'P10',
            'A11', 'B11', 'C11', 'D11', 'E11', 'F11', 'G11', 'H11', 'I11', 'J11', 'K11', 'L11', 'M11', 'N11', 'O11', 'P11',
            'A12', 'B12', 'C12', 'D12', 'E12', 'F12', 'G12', 'H12', 'I12', 'J12', 'K12', 'L12', 'M12', 'N12', 'O12', 'P12',
            'A13', 'B13', 'C13', 'D13', 'E13', 'F13', 'G13', 'H13', 'I13', 'J13', 'K13', 'L13', 'M13', 'N13', 'O13', 'P13',
            'A14', 'B14', 'C14', 'D14', 'E14', 'F14', 'G14', 'H14', 'I14', 'J14', 'K14', 'L14', 'M14', 'N14', 'O14', 'P14',
            'A15', 'B15', 'C15', 'D15', 'E15', 'F15', 'G15', 'H15', 'I15', 'J15', 'K15', 'L15', 'M15', 'N15', 'O15', 'P15',
            'A16', 'B16', 'C16', 'D16', 'E16', 'F16', 'G16', 'H16', 'I16', 'J16', 'K16', 'L16', 'M16', 'N16', 'O16', 'P16',
            'A17', 'B17', 'C17', 'D17', 'E17', 'F17', 'G17', 'H17', 'I17', 'J17', 'K17', 'L17', 'M17', 'N17', 'O17', 'P17',
            'A18', 'B18', 'C18', 'D18', 'E18', 'F18', 'G18', 'H18', 'I18', 'J18', 'K18', 'L18', 'M18', 'N18', 'O18', 'P18',
            'A19', 'B19', 'C19', 'D19', 'E19', 'F19', 'G19', 'H19', 'I19', 'J19', 'K19', 'L19', 'M19', 'N19', 'O19', 'P19',
            'A20', 'B20', 'C20', 'D20', 'E20', 'F20', 'G20', 'H20', 'I20', 'J20', 'K20', 'L20', 'M20', 'N20', 'O20', 'P20',
            'A21', 'B21', 'C21', 'D21', 'E21', 'F21', 'G21', 'H21', 'I21', 'J21', 'K21', 'L21', 'M21', 'N21', 'O21', 'P21',
            'A22', 'B22', 'C22', 'D22', 'E22', 'F22', 'G22', 'H22', 'I22', 'J22', 'K22', 'L22', 'M22', 'N22', 'O22', 'P22',
            'A23', 'B23', 'C23', 'D23', 'E23', 'F23', 'G23', 'H23', 'I23', 'J23', 'K23', 'L23', 'M23', 'N23', 'O23', 'P23',
            'A24', 'B24', 'C24', 'D24', 'E24', 'F24', 'G24', 'H24', 'I24', 'J24', 'K24', 'L24', 'M24', 'N24', 'O24', 'P24')
  idx = 1:length(wells)
  names(idx) = wells
  return(idx)
}

#' Convert between wellID and column-num
#'
#' Useful for converting between WellIDs (eg., "A2")
#' and well position in a plate (eg., 9)
#'
#' @param x A vector of well IDs
#' @param plate_type Either 96-well or 384-well
#' @return A vector of plate positions
#' @export
well2index = function(x, plate_type='96-well'){
  x = gsub('([A-Z])0([0-9])', '\\1\\2', as.character(x))
  if(plate_type == '96-well'){
    idx = .well96_index()
  } else
    if(plate_type == '384-well'){
      idx = .well384_index()
    } else {
      stop('Do not recoginize plate type')
    }
  return(as.numeric(idx[x]))
}