Calculate FP per cell values — calc

Takes as input plate reader data processed with process_plate() and uses normalised/calibrated values to calculate per-cell values. Adds column(s) for FP/cell as either: (a) normalisedFP/normalisedOD (RFU/OD), (b) calibratedFP/calibratedOD (molecules/cell). Plots results and returns a dataframe. Note that technically, units of molecules are 'molecules of equivalent FP' and cells are 'particles of equivalent microspheres'.

Usage

calc_fppercell(
  data_csv,
  timecourse = TRUE,
  flu_channels,
  flu_labels,
  remove_wells,
  get_rfu_od = TRUE,
  get_mol_cell = FALSE,
  plate_type = 96,
  outfolder = "."
)

Arguments

data_csv: path to a CSV file containing processed plate reader data
timecourse: logical. Is the data timecourse/kinetic data and does it include a variable called 'time'?
flu_channels: the column names for the NORMALISED fluorescence data
flu_labels: the column names for the CALIBRATED fluorescence data
remove_wells: list of coordinates of wells to be removed from analysis (e.g. empty wells)
get_rfu_od: logical. if TRUE, uses normalised_FP and normalised_OD to calculate FP per cell as FP/OD in relative fluorescence units/relative OD (RFU/OD).
get_mol_cell: logical. if TRUE, uses calibrated_FP and calibrated_OD to calculate FP per cell as FP/OD in relative fluorescence units/relative OD (molecules/cell).
plate_type: type of plate. numeric, i.e. '96' for 96-well plate. Defines the rows and columns used for plotting figures. Defaults to '96'.
outfolder: path to folder where output files should be saved. Defaults to current working directory.

Value

a data.frame with columns for each FP/cell calculation

Examples

if (FALSE) {
  pc_data_mCherry <- calc_fppercell(
    data_csv = "mcherry_parsed_processed.csv",
    flu_channels = c("red1red1"), flu_labels = c("mCherry"),
    remove_wells = c("A11"),
    get_rfu_od = TRUE, get_mol_cell = TRUE,
    outfolder = file.path("plots")
  )
}