wrapperWPM: Generate plate plans in a single step
In wpm: Well Plate Maker

Description Usage Arguments Value Examples

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.

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

`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.

a dataframe if wpm finds a solution.

# 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")