Plot plate data (Heatmap + Dose Ranks + Smart Legend + Explicit QC)

Usage

plot_plate_stack_info(
  dt_plate,
  ctrl_fail_threshold = 0.6,
  n_sd = 1,
  use_sd_threshold = TRUE,
  items_per_line = 6
)

Arguments

dt_plate: data.table. Input data containing plate layout, measurements, and standard gDR identifiers.
ctrl_fail_threshold: numeric (Default: 0.6). Flags control wells with a readout below Mean(Controls) * ctrl_fail_threshold.
n_sd: numeric (Default: 1). Sets the upper limit for flagging high signals using the formula Mean(Controls) + (n_sd * SD(Controls)).
use_sd_threshold: logical (Default: TRUE). If TRUE, uses the dynamic SD-based limit defined by n_sd. If FALSE, uses a fixed limit of Mean(Controls) * 1.1.
items_per_line: integer. Number of doses to show per line in the legend. Default 6.

Value

A named list of ggplot objects for each barcode

Author

Bartosz Czech czech.bartosz@external.gene.com

Examples

conc_series <- c(0, 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, 10)

test_data <- data.table::data.table(
   WellColumn = sprintf("%02d", rep(1:12, each = 8)),
   WellRow = rep(LETTERS[1:8], times = 12),
   Barcode = rep(c("Plate_1", "Plate_2"), each = 48),
   clid = "CellLineA"
)

invisible(test_data[, Concentration := rep(rep(conc_series, length.out = 48), 2)])
invisible(test_data[, Gnumber := ifelse(Concentration == 0, "vehicle", "Drug_A")])
invisible(test_data[Gnumber == "vehicle", Concentration := 0])

invisible(test_data[, ReadoutValue := ifelse(Gnumber == "vehicle",
                                    rnorm(.N, 1000, 50),
                                    rnorm(.N, 500, 100))])
library(ggtext)
plots <- plot_plate_stack_info(test_data)
plots[[1]]


combo_data <- data.table::copy(test_data)
invisible(combo_data[, Barcode := "Plate_Combo"])
invisible(combo_data[, Concentration_2 := rep(rev(conc_series), length.out = .N)])
invisible(combo_data[, Gnumber_2 := ifelse(Concentration_2 == 0, "vehicle", "Drug_B")])
invisible(combo_data[Gnumber_2 == "vehicle", Concentration_2 := 0])

combo_plots <- plot_plate_stack_info(combo_data)
combo_plots[[1]]