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hotfix plate wrapper #49

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hotfix plate wrapper #49

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Set p = 1, penalize_lines = "none" for plate scoring functions in op…
julianesiebourg Jul 9, 2024
cedd39f
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julianesiebourg Jul 9, 2024
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11 changes: 7 additions & 4 deletions R/score_plates.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@


#' Internal helper function to set up an (n m) x (n m) pairwise distance matrix for a plate with n rows and m columns
#'
#' @param plate_x Dimension of plate in x direction (i.e number of columns)
Expand Down Expand Up @@ -99,7 +97,6 @@ mk_plate_scoring_functions <- function(batch_container, plate = NULL, row, colum
)

plate_scoring_func <- function(samples, plate, plate_name, row, column, group) {

# Have to distinguish between empty positions on plate and NA-levels of experimental factors which may happen for real samples, too
nonempty_pos <- !is.na(samples[[".sample_id"]])

Expand Down Expand Up @@ -250,7 +247,13 @@ optimize_multi_plate_design <- function(batch_container, across_plates_variables

if (!is.null(within_plate_variables)) {
plate_levels <- unique(bc$get_locations()[[plate]])
scoring_funcs <- purrr::map(within_plate_variables, ~ mk_plate_scoring_functions(bc, plate = plate, row = row, column = column, group = .x)) |>
scoring_funcs <- purrr::map(
within_plate_variables,
~ mk_plate_scoring_functions(bc,
plate = plate, row = row, column = column, group = .x,
p = 1, penalize_lines = "none"
)
) |>
unlist()
names(scoring_funcs) <- paste(rep(within_plate_variables, each = length(plate_levels)), names(scoring_funcs))

Expand Down