Plot a single plate's stack info — plot_single_plate_stack

Generates the QC and dose-rank heatmap for a single plate subset. Handles all necessary data transformations (factor conversion, ranking, color mapping) internally.

Usage

plot_single_plate_stack_info(
  dt_subset,
  plate_id = NULL,
  drug_color_mapping = NULL,
  ctrl_fail_threshold = 0.6,
  n_sd = 1,
  use_sd_threshold = TRUE,
  items_per_line = 6
)

Arguments

dt_subset: data.table. Subset of the plate data corresponding to a single barcode/plate.
plate_id: character (Optional). The identifier (barcode) of the plate. If NULL, attempts to extract it from the data.
drug_color_mapping: character (Optional). Named vector of color codes. If NULL, generated automatically.
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 ggplot object.

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 = rep(1:12, each = 8),
   WellRow = rep(LETTERS[1:8], times = 12),
   clid = "CellLineA",
   Barcode = "Plate_1"
)

invisible(test_data[, Concentration := rep(conc_series, length.out = .N)])
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, 1000 * (1 / (1 + Concentration)), 50))])

library(ggtext)
plot_single_plate_stack_info(test_data)


invisible(test_data[, Concentration_2 := rep(rev(conc_series), length.out = .N)])
invisible(test_data[, Gnumber_2 := ifelse(Concentration_2 == 0, "vehicle", "Drug_B")])

invisible(test_data[Gnumber_2 == "vehicle", Concentration_2 := 0])

plot_single_plate_stack_info(test_data)