plot_plate function

Plot plate layouts

plot_plate(
  .tbl,
  plate = plate,
  row = row,
  column = column,
  .color,
  .alpha = NULL,
  .pattern = NULL,
  title = paste("Layout by", rlang::as_name(rlang::enquo(plate))),
  add_excluded = FALSE,
  rename_empty = FALSE
)

Arguments

• .tbl: a tibble (or data.frame) with the samples assigned to locations. Alternatively a BatchContainter with samples can be supplied here.
• plate: optional dimension variable used for the plate ids
• row: the dimension variable used for the row ids
• column: the dimension variable used for the column ids
• .color: the continuous or discrete variable to color by
• .alpha: a continuous variable encoding transparency
• .pattern: a discrete variable encoding tile pattern (needs ggpattern)
• title: string for the plot title
• add_excluded: flag to add excluded wells (in bc$exclude) to the plot. A BatchContainer must be provided for this.
• rename_empty: whether NA entries in sample table should be renamed to 'empty`.

Returns

the ggplot object

Examples

nPlate <- 3
nColumn <- 4
nRow <- 6

treatments <- c("CTRL", "TRT1", "TRT2")
timepoints <- c(1, 2, 3)

bc <- BatchContainer$new(
  dimensions = list(
    plate = nPlate,
    column = list(values = letters[1:nColumn]),
    row = nRow
  )
)

sample_sheet <- tibble::tibble(
  sampleID = 1:(nPlate * nColumn * nRow),
  Treatment = rep(treatments, each = floor(nPlate * nColumn * nRow) / length(treatments)),
  Timepoint = rep(timepoints, floor(nPlate * nColumn * nRow) / length(treatments))
)

# assign samples from the sample sheet
bc <- assign_random(bc, samples = sample_sheet)

plot_plate(bc$get_samples(),
  plate = plate, column = column, row = row,
  .color = Treatment, .alpha = Timepoint
)

plot_plate(bc$get_samples(),
  plate = plate, column = column, row = row,
  .color = Treatment, .pattern = Timepoint
)

Author(s)

siebourj