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Added tests for detectSerieOut (#79)
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| ### Test detectSingleOut. | ||
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| ### Test fitSpline | ||
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| Sys.setlocale("LC_COLLATE", "C") | ||
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| ## Read test data from .csv | ||
| testDat <- read.csv("testDat.csv", stringsAsFactors = FALSE) | ||
| # Set Replicate to 1 for all observations of check1 so geno.decomp can | ||
| # actually be used for testing. | ||
| testDat[testDat[["Genotype"]] == "check1", "Replicate"] <- 1 | ||
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| ## Create TP object. | ||
| testTP <- createTimePoints(dat = testDat, experimentName = "testExp", | ||
| genotype = "Genotype", timePoint = "timepoints", | ||
| plotId = "pos", rowNum = "y", colNum = "x") | ||
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| ## Fit models. | ||
| testFitMod <- fitModels(testTP, trait = "t1", quiet = TRUE) | ||
| testFitModGD <- fitModels(testTP, trait = "t1", geno.decomp = "Replicate", | ||
| quiet = TRUE) | ||
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| ## Get corrected values. | ||
| corr <- getCorrected(testFitMod) | ||
| corrGD <- getCorrected(testFitModGD) | ||
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| ## Fit a splines on the corrected values. | ||
| expect_warning(splineRes <- fitSpline(inDat = corr, trait = "t1_corr")) | ||
| expect_warning(splineResGD <- fitSpline(inDat = corrGD, trait = "t1_corr")) | ||
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| ## get coefDat and predDat. | ||
| coefDat <- splineRes[["coefDat"]] | ||
| predDat <- splineRes[["predDat"]] | ||
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| coefDatGD <- splineResGD[["coefDat"]] | ||
| predDatGD <- splineResGD[["predDat"]] | ||
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| ## Check that general checks in detectSingleOut function correctly. | ||
| expect_error(detectSerieOut(trait = 1), | ||
| "trait should be a character string of length 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = 1), | ||
| "corrDat should be a data.frame") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, predDat = 1), | ||
| "predDat should be a data.frame") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = 1), | ||
| "coefDat should be a data.frame") | ||
| expect_error(detectSerieOut(trait = "t2_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat), | ||
| "corrDat should at least contain the following columns") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = coefDat, coefDat = coefDat), | ||
| "predDat should at least contain the following columns") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = predDat), | ||
| "coefDat should at least contain the following columns") | ||
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| ## Check that checks for genotypes function correctly | ||
| expect_warning(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat), | ||
| "have less than 3 plotIds and are skipped in the outlier") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = 1), | ||
| "genotypes should be a character vector") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "a"), | ||
| "all genotypes should be in predDat") | ||
| expect_error(detectSerieOut(trait = "t1_corr", | ||
| corrDat = corr[corr[["genotype"]] != "G12", ], | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "G12"), | ||
| "all genotypes should be in corrDat") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, | ||
| coefDat = coefDat[coefDat[["genotype"]] != "G12", ], | ||
| genotypes = "G12"), | ||
| "all genotypes should be in coefDat") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "G12"), | ||
| "No genotypes left for performing outlier detection") | ||
| expect_silent(serieOut1 <- detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1")) | ||
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| ## Check that general structure of the output is correct. | ||
| expect_inherits(serieOut1, c("serieOut", "data.frame")) | ||
| expect_equal(dim(serieOut1), c(7, 4)) | ||
| expect_equal(colnames(serieOut1), | ||
| c("plotId", "genotype", "reason", "value")) | ||
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| ## Check that full output content is correct. | ||
| expect_equal_to_reference(serieOut1, file = "serieOut") | ||
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| ## Check that parameter thrCor functions correctly. | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrCor = "a"), | ||
| "thrCor should be a numerical vector with values between -1 and 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrCor = 2), | ||
| "thrCor should be a numerical vector with values between -1 and 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrCor = 0:1), | ||
| "thrCor should be a vector of length 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corrGD, | ||
| predDat = predDatGD, coefDat = coefDatGD, | ||
| genotypes = "check1", geno.decomp = "geno.decomp", | ||
| thrCor = 0:1), | ||
| "thrCor should be a named vector, with names matching the levels") | ||
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| ## Check that parameter thrPca functions correctly. | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrPca = "a"), | ||
| "thrPca should be a numerical vector with positive values") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrPca = -1), | ||
| "thrPca should be a numerical vector with positive values") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrPca = 0:1), | ||
| "thrPca should be a vector of length 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corrGD, | ||
| predDat = predDatGD, coefDat = coefDatGD, | ||
| genotypes = "check1", geno.decomp = "geno.decomp", | ||
| thrPca = 0:1), | ||
| "thrPca should be a named vector, with names matching the levels") | ||
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| ## Check that parameter thrPca functions correctly. | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrSlope = "a"), | ||
| "thrSlope should be a numerical vector with values between 0 and 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrSlope = -1), | ||
| "thrSlope should be a numerical vector with values between 0 and 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrSlope = 0:1), | ||
| "thrSlope should be a vector of length 1") | ||
| expect_error(detectSerieOut(trait = "t1_corr", corrDat = corrGD, | ||
| predDat = predDatGD, coefDat = coefDatGD, | ||
| genotypes = "check1", geno.decomp = "geno.decomp", | ||
| thrSlope = 0:1), | ||
| "thrSlope should be a named vector, with names matching the levels") | ||
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| # Set all three to extreme values should result in either 0 or many outliers. | ||
| serieOut2 <- detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrCor = 0, thrPca = 0, | ||
| thrSlope = 1) | ||
| expect_equal(dim(serieOut2), c(9, 4)) | ||
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| serieOut3 <- detectSerieOut(trait = "t1_corr", corrDat = corr, | ||
| predDat = predDat, coefDat = coefDat, | ||
| genotypes = "check1", thrCor = -1, thrPca = 180, | ||
| thrSlope = 0) | ||
| expect_equivalent(serieOut3, data.frame()) | ||
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| ## Check that detecting outliers functions correctly for models with geno.deco | ||
| expect_silent(serieOutGD <- | ||
| detectSerieOut(trait = "t1_corr", corrDat = corrGD, | ||
| predDat = predDatGD, coefDat = coefDatGD, | ||
| genotypes = "check1", geno.decomp = "geno.decomp")) | ||
| expect_equal(dim(serieOutGD), c(6, 5)) | ||
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| ### Check plotting of detectSerieOut results. | ||
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| ## Check that general checks in plot function correctly. | ||
| expect_error(plot(serieOut1, genotypes = "a"), | ||
| "a character vector of genotypes used for outlier detection") | ||
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| ## Check that general output structure is correct. | ||
| expect_silent(p <- plot(serieOut1)) | ||
| expect_inherits(p, "list") | ||
| expect_equal(length(p), 1) | ||
| expect_inherits(p[[1]], "gtable") | ||
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| ## Check that option useTimeNumber functions correctly. | ||
| expect_error(plot(serieOut1, useTimeNumber = TRUE, timeNumber = 1), | ||
| "timeNumber should be a character string of length 1") | ||
| expect_silent(plot(serieOut1, useTimeNumber = TRUE, timeNumber = "timeNumber")) | ||
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| ## Check that option title functions correctly. | ||
| expect_silent(plot(serieOut1, genotypes = "check1", title = "bla")) | ||
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| ## Check that plotting functions correctly with geno.decomp. | ||
| expect_error(plot(serieOutGD, genotypes = "check1", geno.decomp = "2"), | ||
| "All selected geno.decomp levels should be in the data") | ||
| expect_silent(plot(serieOutGD, genotypes = "check1", geno.decomp = "1")) | ||
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| ### Check removal of outliers detected by detectSerieOut | ||
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| ## Check that general checks in plot function correctly. | ||
| expect_error(removeSerieOut(dat = 1), | ||
| "dat should be a data.frame") | ||
| expect_error(removeSerieOut(fitSpline = 1), | ||
| "fitSpline should be an object of class HTPSpline") | ||
| expect_error(removeSerieOut(dat = corr, fitSpline = splineRes), | ||
| "Specify exactly one of dat and fitSpline as inputs") | ||
| expect_error(removeSerieOut(dat = corr[, colnames(corr) != "plotId"]), | ||
| "dat should at least contain the column plotId") | ||
| expect_error(removeSerieOut(dat = corr, serieOut = 1), | ||
| "serieOut should be a data.frame") | ||
| expect_error(removeSerieOut(dat = corr, | ||
| serieOut = serieOut1[, colnames(serieOut1) != "plotId"]), | ||
| "serieOut should at least contain the column plotId") | ||
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| ## Check that outliers are removed from data.frame. | ||
| corrOut1 <- removeSerieOut(dat = corr, serieOut = serieOut1) | ||
| expect_true(all(is.na(corrOut1[corrOut1[["plotId"]] == "c12r1", "t1_corr"]))) | ||
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| corrOut2 <- removeSerieOut(dat = corr, serieOut = serieOut1, | ||
| traits = c("t1", "t1_corr")) | ||
| expect_true(all(is.na(corrOut2[corrOut2[["plotId"]] == "c12r1", | ||
| c("t1", "t1_corr")]))) | ||
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| ## Check that outliers are removed from fitted spline. | ||
| corrOut3 <- removeSerieOut(fitSpline = splineRes, serieOut = serieOut1) | ||
| coefOut3 <- corrOut3$coefDat | ||
| predOut3 <- corrOut3$predDat | ||
| modOut3 <- attr(corrOut3, "modDat") | ||
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| expect_true(all(is.na(coefOut3[coefOut3[["plotId"]] == "c12r1", | ||
| "obj.coefficients"]))) | ||
| expect_true(all(is.na(predOut3[predOut3[["plotId"]] == "c12r1", | ||
| c("pred.value", "deriv", "deriv2")]))) | ||
| expect_true(all(is.na(modOut3[modOut3[["plotId"]] == "c12r1", "t1_corr"]))) | ||
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