# Units test for displaying a blank 1536 well
### Test functions give expected output ###
test_that("functions for displaying a blank 1536 well works", {
blank_plate_schematic <- display_plate(create_blank_plate_1536well())
expect_true(ggplot2::is.ggplot(blank_plate_schematic))
})
# Units test for creating, labeling and displaying a 384 well,
# primer calibration plate with 4 * dilution
### Create dataset of expected function outputs ###
simulated_colkey <- tibble(well_col = factor(1:24),
dilution = rep(c(1, 0.2, 0.04,
0.008, 1, 1),
times = 4),
dilution_nice = rep(c("1x", "5x", "25x",
"125x", "-RT", "NT"),
times = 4),
prep_type = factor(rep(c("+RT", "+RT",
"+RT", "+RT",
"-RT", "NT"),
4),
levels = c("+RT", "-RT", "NT")),
biol_rep = factor(rep(c("A", "B"),
each = 12),
levels = c("A", "B")),
tech_rep = factor(rep(rep(1:2, each = 6),
times = 2))) %>%
dplyr::mutate(sample_id = paste(biol_rep, dilution_nice, sep = "_"))
simulated_rowkey <- tibble(well_row = factor(LETTERS[1:16]),
target_id = c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"))
simulated_label_plate <- tibble(well = paste0(rep(LETTERS[1:16], each = 24),
rep(1:24, times = 16)),
well_row = factor(rep(LETTERS[1:16],
each = 24)),
well_col = factor(rep(1:24, times = 16)),
dilution = rep(c(1, 0.2, 0.04,
0.008, 1, 1),
times = 64),
dilution_nice = rep(c("1x", "5x", "25x",
"125x", "-RT", "NT"),
times = 64),
prep_type = factor(rep(c("+RT", "+RT", "+RT",
"+RT", "-RT", "NT"),
times = 64),
levels = c("+RT", "-RT", "NT")),
biol_rep = factor(rep(rep(c("A", "B"),
each = 12),
times = 16),
levels = c("A", "B")),
tech_rep = factor(rep(rep(1:2, each = 6),
times = 32)),
sample_id = paste(biol_rep, dilution_nice, sep = "_"),
target_id = rep(c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"),
each = 24))
### Test functions give expected output ###
test_that("functions for creating a 384 well, primer calibration plate work with 4 * dilution", {
calculated_blank_384_plate <- create_blank_plate()
calculated_colkey <- create_colkey_4diln_2ctrl_in_24() %>%
dplyr::mutate(sample_id = paste(biol_rep, dilution_nice, sep = "_"))
calculated_rowkey <- create_rowkey_8_in_16_plain(target_id = c("Target_1", "Target_2",
"Target_3", "Target_4",
"Target_5", "Target_6",
"Target_7", "Target_8"))
calculated_labeled_384_plate <- label_plate_rowcol(calculated_blank_384_plate,
calculated_rowkey,
calculated_colkey)
calculated_plate_empty <- display_plate(calculated_labeled_384_plate)
calculated_plate_schematic <- display_plate_qpcr(calculated_labeled_384_plate)
calculated_plate_value <- display_plate_value(calculated_labeled_384_plate,
value = "dilution")
expect_equal(calculated_colkey,
simulated_colkey)
expect_equal(calculated_rowkey,
simulated_rowkey)
expect_equal(calculated_labeled_384_plate,
simulated_label_plate)
expect_true(ggplot2::is.ggplot(calculated_plate_empty))
expect_true(ggplot2::is.ggplot(calculated_plate_schematic))
expect_true(ggplot2::is.ggplot(calculated_plate_value))
})
# Unit test for creating, labeling and displaying a 384 well,
# primer calibration plate with 6 * dilution
### Create dataset of expected function outputs ###
simulated_colkey <- tibble(well_col = factor(1:24),
dilution = rep(c(1, 0.2, 0.04, 0.008,
0.0016, 0.00032, 1, 1),
times = 3),
dilution_nice = rep(c("1x", "5x", "25x", "125x",
"625x", "3125x", "-RT", "NT"),
times = 3),
prep_type = factor(rep(c("+RT", "+RT", "+RT", "+RT",
"+RT", "+RT", "-RT", "NT"),
times = 3),
levels = c("+RT", "-RT", "NT")),
tech_rep = factor(rep(rep(1:3, each = 8)))) %>%
dplyr::mutate(sample_id = paste(dilution_nice, tech_rep, sep = "_"))
simulated_rowkey <- tibble(well_row = factor(LETTERS[1:16]),
target_id = c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"))
simulated_label_plate <- tibble(well = paste0(rep(LETTERS[1:16], each = 24),
rep(1:24, times = 16)),
well_row = factor(rep(LETTERS[1:16], each = 24)),
well_col = factor(rep(1:24, times = 16)),
dilution = rep(c(1, 0.2, 0.04, 0.008,
0.0016, 0.00032, 1, 1),
times = 48),
dilution_nice = rep(c("1x", "5x", "25x", "125x",
"625x", "3125x", "-RT", "NT"),
times = 48),
prep_type = factor(rep(c("+RT", "+RT", "+RT", "+RT",
"+RT", "+RT", "-RT", "NT"),
times = 48),
levels = c("+RT", "-RT", "NT")),
tech_rep = factor(rep(rep(1:3, each = 8),
times = 16)),
sample_id = paste(dilution_nice, tech_rep, sep = "_"),
target_id = rep(c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"),
each = 24))
### Test functions give expected output ###
test_that("functions for creating a 384 well, primer calibration plate work with 6 * dilution", {
calculated_blank_384_plate <- create_blank_plate()
calculated_colkey <- create_colkey_6diln_2ctrl_in_24() %>%
dplyr::mutate(sample_id = paste(dilution_nice, tech_rep, sep = "_"))
calculated_rowkey <- create_rowkey_8_in_16_plain(target_id = c("Target_1", "Target_2",
"Target_3", "Target_4",
"Target_5", "Target_6",
"Target_7", "Target_8"))
calculated_labeled_384_plate <- label_plate_rowcol(calculated_blank_384_plate,
calculated_rowkey,
calculated_colkey)
expect_equal(calculated_colkey,
simulated_colkey)
expect_equal(calculated_rowkey,
simulated_rowkey)
expect_equal(calculated_labeled_384_plate,
simulated_label_plate)
})
# Unit test for creating standard 24 by 16 384 well plate
# with tech reps across rows
### Create dataset of expected function outputs ###
# colkey has well_col a number not a factor, testing coercion
simulated_colkey_6_in_24 <-
tibble(well_col = 1:24,
biol_rep = factor(rep(c("A", "B",
"C", "D"),
each = 6),
levels = c("A", "B",
"C", "D")),
sample_id = rep(c("Sample_1", "Sample_2",
"Sample_3", "Sample_4",
"Sample_5", "Sample_6"),
times = 4))
simulated_rowkey_4_in_16 <-
tibble(well_row = factor(LETTERS[1:16]),
prep_type = factor(rep(c("+RT", "+RT",
"+RT", "-RT"),
each = 4),
levels = c("+RT", "-RT")),
tech_rep = factor(rep(c(1, 2, 3, 1),
each = 4),
levels = c(1:3)),
target_id = rep(c("Target_1", "Target_2",
"Target_3", "Target_4"),
times = 4))
simulated_labeled_384_plate_row4_in_16 <-
tibble(well = paste0(rep(LETTERS[1:16], each = 24),
rep(1:24, times = 16)),
well_row = factor(rep(LETTERS[1:16], each = 24)),
well_col = factor(rep(1:24, times = 16)),
biol_rep = factor(rep(rep(c("A", "B",
"C", "D"),
each = 6),
times = 16),
levels = c("A", "B",
"C", "D")),
sample_id = rep(c("Sample_1", "Sample_2",
"Sample_3", "Sample_4",
"Sample_5", "Sample_6"),
times = 64),
prep_type = factor(rep(c("+RT", "+RT",
"+RT", "-RT"),
each = 96),
levels = c("+RT", "-RT")),
tech_rep = factor(c(rep(1:3, each = 96),
rep(1, times = 96))),
target_id = rep(rep(c("Target_1", "Target_2",
"Target_3", "Target_4"),
each = 24),
times = 4))
### Test functions give expected output ###
test_that("functions for creating a standard 384 well with tech reps across rows", {
target_id_levels <- c("Target_1", "Target_2",
"Target_3", "Target_4")
calculated_rowkey_4_in_16 <-
create_rowkey_4_in_16(target_id = target_id_levels)
calculated_labeled_384_plate_row4_in_16 <-
label_plate_rowcol(create_blank_plate(),
calculated_rowkey_4_in_16,
simulated_colkey_6_in_24)
expect_equal(calculated_rowkey_4_in_16,
simulated_rowkey_4_in_16)
expect_equal(calculated_labeled_384_plate_row4_in_16,
simulated_labeled_384_plate_row4_in_16)
})
# Unit test for creating standard 24 by 16 384 well plate
# with tech reps across columns
### Create dataset of expected function outputs ###
simulated_colkey_6t_in_24 <-
tibble(well_col = factor(1:24),
prep_type = factor(rep(c("+RT", "+RT",
"+RT", "-RT"),
each = 6),
levels = c("+RT", "-RT")),
tech_rep = factor(rep(c(1, 2, 3, 1),
each = 6),
levels = c(1:3)),
sample_id = rep(c("Sample_1", "Sample_2",
"Sample_3", "Sample_4",
"Sample_5", "Sample_6"),
times = 4))
# rowkey has well_row a character not a factor, testing coercion
simulated_rowkey_T16 <-
tibble(well_row = LETTERS[1:16],
target_id = c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"))
simulated_labeled_384_plate_col6t_in_24 <-
tibble(well = paste0(rep(LETTERS[1:16],
each = 24),
rep(1:24, times = 16)),
well_row = factor(rep(LETTERS[1:16], each = 24)),
well_col = factor(rep(1:24, times = 16)),
prep_type = factor(rep(rep(c("+RT", "+RT",
"+RT", "-RT"),
each = 6),
times = 16),
levels = c("+RT", "-RT")),
tech_rep = factor(rep(rep(c(1:3, 1),
each = 6),
times = 16),
levels = c(1, 2, 3)),
sample_id = rep(c("Sample_1", "Sample_2", "Sample_3",
"Sample_4", "Sample_5", "Sample_6"),
times = 64),
target_id = rep(c("Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8",
"Target_1", "Target_2", "Target_3", "Target_4",
"Target_5", "Target_6", "Target_7", "Target_8"),
each = 24))
### Test functions give expected output ###
test_that("functions for creating a standard 384 well with tech reps across columns", {
sample_id_levels <- c("Sample_1", "Sample_2", "Sample_3",
"Sample_4", "Sample_5", "Sample_6")
calculated_colkey_6t_in_24 <-
create_colkey_6_in_24(sample_id = sample_id_levels)
calculated_labeled_384_plate_col6t_in_24 <-
label_plate_rowcol(create_blank_plate(),
simulated_rowkey_T16,
calculated_colkey_6t_in_24)
expect_equal(calculated_colkey_6t_in_24,
simulated_colkey_6t_in_24)
expect_equal(calculated_labeled_384_plate_col6t_in_24,
simulated_labeled_384_plate_col6t_in_24)
})
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