wrapperWPM {wpm} | R Documentation

## Generate plate plans in a single step

### Description

Wrapper function that generates plate plans like the wpm shiny application. This feature allows the user to use the wpm package from the command line rather than going through a web application.

### Usage

    wrapperWPM(
      user_df,
      plate_dims,
      nb_plates,
      forbidden_wells = NULL,
      buffer_wells = NULL,
      fixed_wells = NULL,
      spatial_constraint = "none",
      max_iteration = 20
    )

### Arguments

`user_df` | dataframe containing user data obtained with the 'convertCSV()' or 'convertESet()' functions.
`plate_dims` | list, containing 2 values: the first is the number of plate's lines and second is the number of plate's columns.
`nb_plates` | numeric, corresponds to the number of plates to fill
`forbidden_wells` | character, the wells that will not be used at all for the experiment. This argument needs to be a character string giving the wells coordinates of the form "LetterNumber" (eg. "A1" for the well positionned in the first row/ first column of the plate).
`buffer_wells` | character, the wells that will be used during experiment but without biological sample in it. Same input structure as for forbidden_wells parameter.
`fixed_wells` | character, the wells that will be used for Quality Control samples or standards during the Experiment. Same input structure as for forbidden_wells parameter.
`spatial_constraint` | character, is the spatial constraint used to place the samples on the plate. It can also be called neighborhood constraint. Currently, the possible values are "none", "NS" (for North-South), "WE" (for West-East) and "NEWS" (North-South-East-West).
`max_iteration` | numeric, maximal number of attemps for wpm to find a valid solution.

### Value

a dataframe if wpm finds a solution.

### Examples

    # create a MSnSet toy example
    sample_names <- c("s1","s2","s3","s4", "s5")
    M <- matrix(NA, nrow = 4, ncol = 5)
    colnames(M) <- sample_names
    rownames(M) <- paste0("id", LETTERS[1:4])
    pd <- data.frame(Environment = rep_len(LETTERS[1:3], 5),
                     Category = rep_len(1:2, 5), row.names = sample_names)
    rownames(pd) <- colnames(M)
    x <- MSnbase::MSnSet(exprs = M,pData =  pd)
    # convert it to a valid dataframe for wpm
    df <- convertESet(x, "Environment")
    # run wpm on the toy example
    wrapperWPM(user_df = df, plate_dims = list(8,12), nb_plates = 1,
               forbidden_wells = "A1,A2,A3", fixed_wells = "B1,B2",
               spatial_constraint = "NS")

[Package wpm version 1.2.1 Index]