plot_plate: Plot plate layouts

In designit: Blocking and Randomization for Experimental Design

Plot plate layouts

Description

Plot plate layouts

Usage

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'.

Value

the ggplot object

Author(s)

siebourj

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
)

designit documentation built on May 29, 2024, 12:04 p.m.