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tests/testthat/test_ID.R
In mpwR: Standardized Comparison of Workflows in Mass Spectrometry-Based Bottom-Up Proteomics
#get_ID_Report
test_that("get_ID_Report works", {
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Generic = list(
filename = "Generic",
software = "Generic",
data = list(
"Generic" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
)
)
)
)
output <- get_ID_Report(input_list = data)
expect_type(output, "list")
expect_equal(length(output), 5)
expect_equal(names(output), c("A", "B", "C", "D", "Generic"))
expect_equal(output[["A"]]$Protein.IDs, c(5, 5))
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
)
)
expect_error(get_ID_Report(input_list = data))
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
# Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
# ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
)
)
expect_error(get_ID_Report(input_list = data))
})
#plot_ID_barplot
test_that("plot_ID_barplot works", {
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
)
)
output <- plot_ID_barplot(input_list = data, level = "Precursor.IDs")
expect_type(output, "list")
expect_s3_class(output[["A"]], "ggplot")
expect_s3_class(output[["B"]], "ggplot")
#test error messages
expect_error(plot_ID_barplot(input_list = data, level = "Preursor.IDs"), "Please check your level entry - only use Precursor.IDs, Peptide.IDs, Protein.IDs or ProteinGroup.IDs")
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
)
)
#test error messages
expect_error(plot_ID_barplot(input_list = data, level = "Precursor.IDs"), "Wrong input detected - each input report requires the following columns Analysis, Run, ProteinGroup.IDs, Protein.IDs, Peptide.IDs, Precursor.IDs")
})
#plot_ID_boxplot
test_that("plot_ID_boxplot works", {
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(NA, NA, NA),
ProteinGroup.IDs = c(487, 490, 486)
)
)
output <- plot_ID_boxplot(input_list = data, level = "Precursor.IDs")
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "Peptide.IDs")
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "Protein.IDs") #NAs are removed - B Analysis not shown
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "ProteinGroup.IDs")
expect_s3_class(output, "ggplot")
#test error messages
expect_error(plot_ID_boxplot(input_list = data, level = "Preursor.IDs"), "Please check your level entry - only use Precursor.IDs, Peptide.IDs, Protein.IDs or ProteinGroup.IDs")
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(NA, NA, NA),
ProteinGroup.IDs = c(487, 490, 486)
)
)
#test error messages
expect_error(plot_ID_boxplot(input_list = data, level = "Precursor.IDs"), "Wrong input detected - each input report requires the following columns Analysis, Run, ProteinGroup.IDs, Protein.IDs, Peptide.IDs, Precursor.IDs")
})
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#get_ID_Report
test_that("get_ID_Report works", {
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Generic = list(
filename = "Generic",
software = "Generic",
data = list(
"Generic" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
)
)
)
)
output <- get_ID_Report(input_list = data)
expect_type(output, "list")
expect_equal(length(output), 5)
expect_equal(names(output), c("A", "B", "C", "D", "Generic"))
expect_equal(output[["A"]]$Protein.IDs, c(5, 5))
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
)
)
expect_error(get_ID_Report(input_list = data))
data <- list(
MQ = list(
filename = "A",
software = "MaxQuant",
data = list(
"ev" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 5),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 2),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 2)
),
"pep" = tibble::tibble(
"Stripped.Sequence_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
),
"pg" = tibble::tibble(
"ProteinGroup.IDs_mpwR" = c("A", "B", "C", "D", "E"),
"Intensity 01" = c(4, 4, 3.9, 5, 5),
"Intensity 02" = c(4, 4, 3.9, 5, 5)
)
)
),
DIANN = list(
filename = "B",
software = "DIA-NN",
data = list(
"DIA-NN" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
),
Spectronaut = list(
filename = "C",
software = "Spectronaut",
data = list(
"Spectronaut" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 15),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6)
)
)
),
PD = list(
filename = "D",
software = "PD",
data = list(
"psm" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
# Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"prot" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
),
"pg" = tibble::tibble(
Run_mpwR = rep(c("A","B"), times = 10),
# ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
)
)
)
)
expect_error(get_ID_Report(input_list = data))
})
#plot_ID_barplot
test_that("plot_ID_barplot works", {
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
)
)
output <- plot_ID_barplot(input_list = data, level = "Precursor.IDs")
expect_type(output, "list")
expect_s3_class(output[["A"]], "ggplot")
expect_s3_class(output[["B"]], "ggplot")
#test error messages
expect_error(plot_ID_barplot(input_list = data, level = "Preursor.IDs"), "Please check your level entry - only use Precursor.IDs, Peptide.IDs, Protein.IDs or ProteinGroup.IDs")
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
)
)
#test error messages
expect_error(plot_ID_barplot(input_list = data, level = "Precursor.IDs"), "Wrong input detected - each input report requires the following columns Analysis, Run, ProteinGroup.IDs, Protein.IDs, Peptide.IDs, Precursor.IDs")
})
#plot_ID_boxplot
test_that("plot_ID_boxplot works", {
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(NA, NA, NA),
ProteinGroup.IDs = c(487, 490, 486)
)
)
output <- plot_ID_boxplot(input_list = data, level = "Precursor.IDs")
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "Peptide.IDs")
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "Protein.IDs") #NAs are removed - B Analysis not shown
expect_s3_class(output, "ggplot")
output <- plot_ID_boxplot(input_list = data, level = "ProteinGroup.IDs")
expect_s3_class(output, "ggplot")
#test error messages
expect_error(plot_ID_boxplot(input_list = data, level = "Preursor.IDs"), "Please check your level entry - only use Precursor.IDs, Peptide.IDs, Protein.IDs or ProteinGroup.IDs")
data <- list(
"A" = tibble::tibble(
Analysis = c("A", "A", "A"),
Run = c("R01", "R02", "R03"),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(538, 542, 538),
ProteinGroup.IDs = c(487, 490, 486)
),
"B" = tibble::tibble(
Analysis = c("B", "B", "B"),
Run = c("R01", "R02", "R03"),
Precursor.IDs = c(4597, 4602, 4585),
Peptide.IDs = c(3194, 3200, 3185),
Protein.IDs = c(NA, NA, NA),
ProteinGroup.IDs = c(487, 490, 486)
)
)
#test error messages
expect_error(plot_ID_boxplot(input_list = data, level = "Precursor.IDs"), "Wrong input detected - each input report requires the following columns Analysis, Run, ProteinGroup.IDs, Protein.IDs, Peptide.IDs, Precursor.IDs")
})
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