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tests/testthat/test_peakPantheR_singleFileSearch.R
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments
context('peakPantheR_singleFileSearch()')
skip_if_not_installed('faahKO', minimum_version = '1.18.0')
library(faahKO)
# remove Rplots.pdf created by ggplot2
on.exit( tryCatch({ file.remove('./Rplots.pdf') }, error=function(e){ invisible() }, warning=function(w){ invisible() }) )
## Input and expected data
# use ko15.CDf file from the pkg faahKO
singleSpectraDataPath <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
tmp_raw_data <- MSnbase::readMSData(singleSpectraDataPath, centroided=TRUE, mode='onDisk')
# targeted features in faahKO
input_ROI <- data.frame(matrix(vector(), 4, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
input_ROI[1,] <- c("ID-1", "testCpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_ROI[2,] <- c("ID-2", "testCpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_ROI[3,] <- c("ID-3", "testCpd 3", 3420., 3454.435, 3495., 464.195358, 464.2, 464.204642)
input_ROI[4,] <- c("ID-4", "testCpd 4", 3670., 3701.697, 3745., 536.194638, 536.2, 536.205362)
input_ROI[,3:8] <- vapply(input_ROI[,3:8], as.numeric, FUN.VALUE=numeric(4))
# found peakTable
found_peakTable <- data.frame(matrix(vector(), 4, 17, dimnames=list(c(), c("found", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax", "peakArea", "maxIntMeasured", "maxIntPredicted", "cpdID", "cpdName", "is_filled", "ppm_error", "rt_dev_sec", "tailingFactor", "asymmetryFactor"))),stringsAsFactors=FALSE)
found_peakTable[1,] <- c(TRUE, 3309.7589296586070, 3346.8277590361445, 3385.4098874628098, 522.194778, 522.20001220703125, 522.205222, 26133726.6811244078, 889280, 901015.80529226747, 'ID-1', 'testCpd 1', FALSE, 0.023376160866574614, 1.93975903614455092, 1.0153573486330891, 1.0268238825675249)
found_peakTable[2,] <- c(TRUE, 3345.3766648628907, 3386.5288072289159, 3428.2788374983961, 496.20001220703125, 496.20001220703125, 496.20001220703125, 35472141.3330242932, 1128960, 1113576.69008227298, 'ID-2', 'testCpd 2', FALSE, 0.024601030353423384, 0.95180722891564074, 1.0053782620427065, 1.0093180792278085)
found_peakTable[3,] <- c(TRUE, 3451.2075903614455, 3451.5072891566265, 3501.6697504924518, 464.195358, 464.20001220703125, 464.204642, 7498427.1583901159, 380736, 389632.13549519412, 'ID-3', 'testCpd 3', FALSE, 0.026296922148575364, -2.92771084337346110, 207.6939219686769036, 380.5019028782010082)
found_peakTable[4,] <- c(TRUE, 3670.9201232710743, 3704.1427831325304, 3740.0172511251831, 536.20001220703125, 536.20001220703125, 536.20001220703125, 8626279.9788195733, 330176, 326763.87246511364, 'ID-4', 'testCpd 4', FALSE, 0.022765817240815486, 2.44578313253032320, 1.0305289730128095, 1.0536948855480386)
found_peakTable[,c(1,13)] <- vapply(found_peakTable[,c(1,13)], as.logical, FUN.VALUE=logical(4))
found_peakTable[,c(2:10,14:17)] <- vapply(found_peakTable[,c(2:10,14:17)], as.numeric, FUN.VALUE=numeric(4))
# found curveFit
cFit1 <- list(amplitude=162404.8057918259, center=3341.888, sigma=0.078786133031045896, gamma=0.0018336101984172684, fitStatus=2, curveModel="skewedGaussian")
class(cFit1) <- 'peakPantheR_curveFit'
cFit2 <- list(amplitude=199249.10572753669, center=3382.577, sigma=0.074904415304607966, gamma=0.0011471899372353885, fitStatus=2, curveModel="skewedGaussian")
class(cFit2) <- 'peakPantheR_curveFit'
cFit3 <- list(amplitude=31645.961277502651, center=3451.435, sigma=0.064803553287811053, gamma=2.8557893789555022, fitStatus=2, curveModel="skewedGaussian")
class(cFit3) <- 'peakPantheR_curveFit'
cFit4 <- list(amplitude=59193.591103772116, center=3698.697, sigma=0.082789238806238355, gamma=0.0026044299691057823, fitStatus=2, curveModel="skewedGaussian")
class(cFit4) <- 'peakPantheR_curveFit'
found_curveFit <- list(cFit1, cFit2, cFit3, cFit4)
# found ROIsDataPoint
found_ROIsDataPoints <- extractSignalRawData(tmp_raw_data, rt=input_ROI[,c('rtMin','rtMax')], mz=input_ROI[,c('mzMin','mzMax')], verbose=FALSE)
test_that('no peakStatistic, no plotEICsPath, no getAcquTime, no FIR, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('peakStatistic, no plotEICsPath, no getAcquTime, no FIR, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=TRUE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('no peakStatistic, no plotEICsPath, with getAcquTime, no FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Check input, mzMLPath must be a .mzML\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=TRUE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (can't check timing)
expect_equal(length(result_singleFileSearch$messages), 8)
expect_equal(result_singleFileSearch$messages[c(1:3,5,6)], expected_messages)
})
test_that('no peakStatistic, with plotEICsPath, no getAcquTime, no FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# temporary file
savePath <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.png')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=savePath, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check plot has been produced
expect_true(file.exists(savePath))
# Check messages (can't check timing and save path)
expect_equal(length(result_singleFileSearch$messages), 8)
expect_equal(result_singleFileSearch$messages[c(1,2,4,5)], expected_messages)
})
test_that('peakStatistic, plotEICsPath, getAcquTime, FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Check input, mzMLPath must be a .mzML\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# temporary file
savePath2 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.png')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=TRUE, plotEICsPath=savePath2, getAcquTime=TRUE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check plot has been produced
expect_true(file.exists(savePath2))
# Check messages (can't check timing and save path)
expect_equal(length(result_singleFileSearch$messages), 10)
expect_equal(result_singleFileSearch$messages[c(1:3,5,6)], expected_messages)
})
test_that('change peak fitting params with ..., no peakStatistic, no plotEICsPath, no getAcquTime, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
expected_peakTable[3,2:10] <- c(3418.0076795585401, 3455.6277710843374, 3495.4734240188186, 464.195358, 464.2000122, 464.204642, 11307215.264967661, 380736, 381327.26552768378)
# Expected curveFit
expected_curveFit <- found_curveFit
expected_curveFit[[3]]$amplitude <- 64246.052173667762
expected_curveFit[[3]]$center <- 3450
expected_curveFit[[3]]$sigma <- 0.07533469863886906
expected_curveFit[[3]]$gamma <- 0.0019238229766131536
expected_curveFit[[3]]$fitStatus <- 2
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# Modify fit of window #3
tmp_params <- list(init_params = list(amplitude=1E5, center=3455., sigma=0.1, gamma=0),
lower_bounds = list(amplitude=0, center=3450., sigma=0, gamma=-0.1),
upper_bounds = list(amplitude=1E9, center=3460., sigma=5, gamma=0.1))
new_params <- list('guess', 'guess', tmp_params, 'guess')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE, params=new_params))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-5)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('no targetFeatures on import, no peakStatistic', {
# Empty targetFeatures
empty_ROI <- data.frame(matrix(vector(), 0, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 0, 13, dimnames=list(c(), c('cpdID', 'cpdName', 'found', 'rt', 'rtMin', 'rtMax', 'mz', 'mzMin', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'is_filled'))), stringsAsFactors=FALSE)
# Expected curveFit
expected_curveFit <- list()
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list()
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 0 windows\n", "No data exist for the rt provided\n", "- No target features passed in 'targetFeatTable', no integration, only TIC will be reported -\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, empty_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 5)
expect_equal(result_singleFileSearch$messages[1:4], expected_messages)
})
test_that('no targetFeatures on import, peakStatistic', {
# Empty targetFeatures
empty_ROI <- data.frame(matrix(vector(), 0, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 0, 17, dimnames=list(c(), c('cpdID', 'cpdName', 'found', 'rt', 'rtMin', 'rtMax', 'mz', 'mzMin', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'is_filled', 'ppm_error', 'rt_dev_sec', 'tailingFactor', 'asymmetryFactor'))), stringsAsFactors=FALSE)
# Expected curveFit
expected_curveFit <- list()
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list()
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 0 windows\n", "No data exist for the rt provided\n", "- No target features passed in 'targetFeatTable', no integration, only TIC will be reported -\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, empty_ROI, peakStatistic=TRUE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 5)
expect_equal(result_singleFileSearch$messages[1:4], expected_messages)
})
test_that('no features found, no FIR', {
# targetFeature that doesn't give result
noMatch_ROI <- input_ROI[1,]
noMatch_ROI[1, 6:8] <- c(52.194778, 52.2, 52.205222)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 1, 13, dimnames=list(c(), c('found', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'cpdID', 'cpdName', 'is_filled'))), stringsAsFactors=FALSE)
expected_peakTable$cpdID <- "ID-1"
expected_peakTable$cpdName <- "testCpd 1"
expected_peakTable$found <- FALSE
expected_peakTable$is_filled <- FALSE
# Expected curveFit
expected_curveFit <- list(NA)
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list(data.frame(rt=numeric(), mz=numeric(), int=numeric(), stringsAsFactors=FALSE))
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c( "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 1 windows\n", "Fit of ROI #1 is unsuccessful (try error)\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, noMatch_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 6)
expect_equal(result_singleFileSearch$messages[c(1,2,4)], expected_messages)
})
test_that('one feature not found (#3), use FIR', {
# input ROI, no window #3
tmp_ROI <- input_ROI
tmp_ROI[3,c('mzMin','mz','mzMax')] <- c(46.19, 46.2, 46.21)
# input FIR (use previously found peaks dimension. Need to widen mz as this test data doesn't give any mz width)
input_FIR <- found_peakTable[,c("mzMin", "mzMax", "rtMin", "rtMax")]
input_FIR$mzMin <- input_FIR$mzMin - 0.0005
input_FIR$mzMax <- input_FIR$mzMax + 0.0005
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
expected_peakTable[3,c('rtMin','rt', 'rtMax', 'mzMin', 'mz', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted')] <- c(3451.20759036145, 3454.435, 3501.66975049245, 464.194858, 464.2, 464.205142, 7799325, 380736, as.numeric(NA))
expected_peakTable$found[3] <- TRUE
expected_peakTable$is_filled[3] <- TRUE
# Expected curveFit
expected_curveFit <- found_curveFit
expected_curveFit[[3]] <- NA
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
expected_ROIsDataPoint[[3]] <- data.frame(rt=numeric(), mz=numeric(), int=numeric(), stringsAsFactors=FALSE)
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Fit of ROI #3 is unsuccessful (try error)\n", "1 features to integrate with FIR\n", "Reading data from 1 windows\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, tmp_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=input_FIR, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (can't check timing)
expect_equal(length(result_singleFileSearch$messages), 11)
expect_equal(result_singleFileSearch$messages[c(1,2,4,5,7,8)], expected_messages)
})
test_that('raise errors', {
# paths to trigger errors
fakeInputPath <- './notAPath/test.CDF'
fakeOutputPath <- './notAPath/save.png'
wrongOutputFormat <- './notAPNG.txt'
# FIR to trigger errors
notADataFrame <- 'not at dataframe'
wrongNbrows <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(), c("mzMin", "mzMax", "rtMin", "rtMax"))), stringsAsFactors=FALSE)
wrongCols <- data.frame(matrix(vector(), 4, 4, dimnames=list(c(), c("wrongCol name", "mzMax", "rtMin", "rtMax"))), stringsAsFactors=FALSE)
# singleSpectraDataPath doesnt exist
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath=fakeInputPath, input_ROI), "Check input, file*")
# save folder doesnt exist
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, plotEICsPath=fakeOutputPath), "Check input, plotEICsPath folder*")
# save file is not a .png
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, plotEICsPath=wrongOutputFormat), "Check input, plotEICsPath file name*")
# not implemented curveModel
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, curveModel='FakeModel'), "Error: \"curveModel\" must be one of: skewedGaussian, emgGaussian")
# FIR is not a data.frame
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=notADataFrame), "Check input, FIR must be a data.frame not character")
# FIR has wrong number of rows
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=wrongNbrows), "Check input, FIR must have the same number of rows as targetFeatTable")
# FIR columns are wrong
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=wrongCols), 'Check input, FIR must have "mzMin", "mzMax", "rtMin" and "rtMax" as columns')
# rtMin > rtMax
wrong_ROI_rt <- input_ROI
wrong_ROI_rt[2,] <- c("ID-2", "testCpd 2", 3440., 3385.577, 3280., 496.195038, 496.2, 496.204962)
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, wrong_ROI_rt), 'Check input, "rtMin" must be <= to "rtMax"')
# mzMin > mzMax
wrong_ROI_mz <- input_ROI
wrong_ROI_mz[3,] <- c("ID-3", "testCpd 3", 3420., 3454.435, 3495., 464.204642, 464.2, 464.195358)
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, wrong_ROI_mz), 'Check input, "mzMin" must be <= to "mzMax"')
})
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context('peakPantheR_singleFileSearch()')
skip_if_not_installed('faahKO', minimum_version = '1.18.0')
library(faahKO)
# remove Rplots.pdf created by ggplot2
on.exit( tryCatch({ file.remove('./Rplots.pdf') }, error=function(e){ invisible() }, warning=function(w){ invisible() }) )
## Input and expected data
# use ko15.CDf file from the pkg faahKO
singleSpectraDataPath <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
tmp_raw_data <- MSnbase::readMSData(singleSpectraDataPath, centroided=TRUE, mode='onDisk')
# targeted features in faahKO
input_ROI <- data.frame(matrix(vector(), 4, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
input_ROI[1,] <- c("ID-1", "testCpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_ROI[2,] <- c("ID-2", "testCpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_ROI[3,] <- c("ID-3", "testCpd 3", 3420., 3454.435, 3495., 464.195358, 464.2, 464.204642)
input_ROI[4,] <- c("ID-4", "testCpd 4", 3670., 3701.697, 3745., 536.194638, 536.2, 536.205362)
input_ROI[,3:8] <- vapply(input_ROI[,3:8], as.numeric, FUN.VALUE=numeric(4))
# found peakTable
found_peakTable <- data.frame(matrix(vector(), 4, 17, dimnames=list(c(), c("found", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax", "peakArea", "maxIntMeasured", "maxIntPredicted", "cpdID", "cpdName", "is_filled", "ppm_error", "rt_dev_sec", "tailingFactor", "asymmetryFactor"))),stringsAsFactors=FALSE)
found_peakTable[1,] <- c(TRUE, 3309.7589296586070, 3346.8277590361445, 3385.4098874628098, 522.194778, 522.20001220703125, 522.205222, 26133726.6811244078, 889280, 901015.80529226747, 'ID-1', 'testCpd 1', FALSE, 0.023376160866574614, 1.93975903614455092, 1.0153573486330891, 1.0268238825675249)
found_peakTable[2,] <- c(TRUE, 3345.3766648628907, 3386.5288072289159, 3428.2788374983961, 496.20001220703125, 496.20001220703125, 496.20001220703125, 35472141.3330242932, 1128960, 1113576.69008227298, 'ID-2', 'testCpd 2', FALSE, 0.024601030353423384, 0.95180722891564074, 1.0053782620427065, 1.0093180792278085)
found_peakTable[3,] <- c(TRUE, 3451.2075903614455, 3451.5072891566265, 3501.6697504924518, 464.195358, 464.20001220703125, 464.204642, 7498427.1583901159, 380736, 389632.13549519412, 'ID-3', 'testCpd 3', FALSE, 0.026296922148575364, -2.92771084337346110, 207.6939219686769036, 380.5019028782010082)
found_peakTable[4,] <- c(TRUE, 3670.9201232710743, 3704.1427831325304, 3740.0172511251831, 536.20001220703125, 536.20001220703125, 536.20001220703125, 8626279.9788195733, 330176, 326763.87246511364, 'ID-4', 'testCpd 4', FALSE, 0.022765817240815486, 2.44578313253032320, 1.0305289730128095, 1.0536948855480386)
found_peakTable[,c(1,13)] <- vapply(found_peakTable[,c(1,13)], as.logical, FUN.VALUE=logical(4))
found_peakTable[,c(2:10,14:17)] <- vapply(found_peakTable[,c(2:10,14:17)], as.numeric, FUN.VALUE=numeric(4))
# found curveFit
cFit1 <- list(amplitude=162404.8057918259, center=3341.888, sigma=0.078786133031045896, gamma=0.0018336101984172684, fitStatus=2, curveModel="skewedGaussian")
class(cFit1) <- 'peakPantheR_curveFit'
cFit2 <- list(amplitude=199249.10572753669, center=3382.577, sigma=0.074904415304607966, gamma=0.0011471899372353885, fitStatus=2, curveModel="skewedGaussian")
class(cFit2) <- 'peakPantheR_curveFit'
cFit3 <- list(amplitude=31645.961277502651, center=3451.435, sigma=0.064803553287811053, gamma=2.8557893789555022, fitStatus=2, curveModel="skewedGaussian")
class(cFit3) <- 'peakPantheR_curveFit'
cFit4 <- list(amplitude=59193.591103772116, center=3698.697, sigma=0.082789238806238355, gamma=0.0026044299691057823, fitStatus=2, curveModel="skewedGaussian")
class(cFit4) <- 'peakPantheR_curveFit'
found_curveFit <- list(cFit1, cFit2, cFit3, cFit4)
# found ROIsDataPoint
found_ROIsDataPoints <- extractSignalRawData(tmp_raw_data, rt=input_ROI[,c('rtMin','rtMax')], mz=input_ROI[,c('mzMin','mzMax')], verbose=FALSE)
test_that('no peakStatistic, no plotEICsPath, no getAcquTime, no FIR, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('peakStatistic, no plotEICsPath, no getAcquTime, no FIR, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=TRUE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('no peakStatistic, no plotEICsPath, with getAcquTime, no FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Check input, mzMLPath must be a .mzML\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=TRUE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (can't check timing)
expect_equal(length(result_singleFileSearch$messages), 8)
expect_equal(result_singleFileSearch$messages[c(1:3,5,6)], expected_messages)
})
test_that('no peakStatistic, with plotEICsPath, no getAcquTime, no FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# temporary file
savePath <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.png')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=savePath, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check plot has been produced
expect_true(file.exists(savePath))
# Check messages (can't check timing and save path)
expect_equal(length(result_singleFileSearch$messages), 8)
expect_equal(result_singleFileSearch$messages[c(1,2,4,5)], expected_messages)
})
test_that('peakStatistic, plotEICsPath, getAcquTime, FIR, verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable
# Expected curveFit
expected_curveFit <- found_curveFit
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Check input, mzMLPath must be a .mzML\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #3\n")
# temporary file
savePath2 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.png')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=TRUE, plotEICsPath=savePath2, getAcquTime=TRUE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check plot has been produced
expect_true(file.exists(savePath2))
# Check messages (can't check timing and save path)
expect_equal(length(result_singleFileSearch$messages), 10)
expect_equal(result_singleFileSearch$messages[c(1:3,5,6)], expected_messages)
})
test_that('change peak fitting params with ..., no peakStatistic, no plotEICsPath, no getAcquTime, no verbose', {
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
expected_peakTable[3,2:10] <- c(3418.0076795585401, 3455.6277710843374, 3495.4734240188186, 464.195358, 464.2000122, 464.204642, 11307215.264967661, 380736, 381327.26552768378)
# Expected curveFit
expected_curveFit <- found_curveFit
expected_curveFit[[3]]$amplitude <- 64246.052173667762
expected_curveFit[[3]]$center <- 3450
expected_curveFit[[3]]$sigma <- 0.07533469863886906
expected_curveFit[[3]]$gamma <- 0.0019238229766131536
expected_curveFit[[3]]$fitStatus <- 2
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n")
# Modify fit of window #3
tmp_params <- list(init_params = list(amplitude=1E5, center=3455., sigma=0.1, gamma=0),
lower_bounds = list(amplitude=0, center=3450., sigma=0, gamma=-0.1),
upper_bounds = list(amplitude=1E9, center=3460., sigma=5, gamma=0.1))
new_params <- list('guess', 'guess', tmp_params, 'guess')
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=FALSE, params=new_params))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-5)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 1)
expect_equal(result_singleFileSearch$messages, expected_messages)
})
test_that('no targetFeatures on import, no peakStatistic', {
# Empty targetFeatures
empty_ROI <- data.frame(matrix(vector(), 0, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 0, 13, dimnames=list(c(), c('cpdID', 'cpdName', 'found', 'rt', 'rtMin', 'rtMax', 'mz', 'mzMin', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'is_filled'))), stringsAsFactors=FALSE)
# Expected curveFit
expected_curveFit <- list()
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list()
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 0 windows\n", "No data exist for the rt provided\n", "- No target features passed in 'targetFeatTable', no integration, only TIC will be reported -\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, empty_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 5)
expect_equal(result_singleFileSearch$messages[1:4], expected_messages)
})
test_that('no targetFeatures on import, peakStatistic', {
# Empty targetFeatures
empty_ROI <- data.frame(matrix(vector(), 0, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 0, 17, dimnames=list(c(), c('cpdID', 'cpdName', 'found', 'rt', 'rtMin', 'rtMax', 'mz', 'mzMin', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'is_filled', 'ppm_error', 'rt_dev_sec', 'tailingFactor', 'asymmetryFactor'))), stringsAsFactors=FALSE)
# Expected curveFit
expected_curveFit <- list()
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list()
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 0 windows\n", "No data exist for the rt provided\n", "- No target features passed in 'targetFeatTable', no integration, only TIC will be reported -\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, empty_ROI, peakStatistic=TRUE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 5)
expect_equal(result_singleFileSearch$messages[1:4], expected_messages)
})
test_that('no features found, no FIR', {
# targetFeature that doesn't give result
noMatch_ROI <- input_ROI[1,]
noMatch_ROI[1, 6:8] <- c(52.194778, 52.2, 52.205222)
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- data.frame(matrix(vector(), 1, 13, dimnames=list(c(), c('found', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted', 'cpdID', 'cpdName', 'is_filled'))), stringsAsFactors=FALSE)
expected_peakTable$cpdID <- "ID-1"
expected_peakTable$cpdName <- "testCpd 1"
expected_peakTable$found <- FALSE
expected_peakTable$is_filled <- FALSE
# Expected curveFit
expected_curveFit <- list(NA)
# Expected ROIsDataPoint
expected_ROIsDataPoint <- list(data.frame(rt=numeric(), mz=numeric(), int=numeric(), stringsAsFactors=FALSE))
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c( "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 1 windows\n", "Fit of ROI #1 is unsuccessful (try error)\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, noMatch_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=NULL, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (loading file)
expect_equal(length(result_singleFileSearch$messages), 6)
expect_equal(result_singleFileSearch$messages[c(1,2,4)], expected_messages)
})
test_that('one feature not found (#3), use FIR', {
# input ROI, no window #3
tmp_ROI <- input_ROI
tmp_ROI[3,c('mzMin','mz','mzMax')] <- c(46.19, 46.2, 46.21)
# input FIR (use previously found peaks dimension. Need to widen mz as this test data doesn't give any mz width)
input_FIR <- found_peakTable[,c("mzMin", "mzMax", "rtMin", "rtMax")]
input_FIR$mzMin <- input_FIR$mzMin - 0.0005
input_FIR$mzMax <- input_FIR$mzMax + 0.0005
# Expected TIC
expected_TIC <- 2410533091
# Expected peakTable
expected_peakTable <- found_peakTable[,1:13]
expected_peakTable[3,c('rtMin','rt', 'rtMax', 'mzMin', 'mz', 'mzMax', 'peakArea', 'maxIntMeasured', 'maxIntPredicted')] <- c(3451.20759036145, 3454.435, 3501.66975049245, 464.194858, 464.2, 464.205142, 7799325, 380736, as.numeric(NA))
expected_peakTable$found[3] <- TRUE
expected_peakTable$is_filled[3] <- TRUE
# Expected curveFit
expected_curveFit <- found_curveFit
expected_curveFit[[3]] <- NA
# Expected ROIsDataPoint
expected_ROIsDataPoint <- found_ROIsDataPoints
expected_ROIsDataPoint[[3]] <- data.frame(rt=numeric(), mz=numeric(), int=numeric(), stringsAsFactors=FALSE)
# Expected acquTime
expected_acquTime <- NA
# Expected messages
expected_messages <- c("Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Warning: rtMin/rtMax outside of ROI; datapoints cannot be used for mzMin/mzMax calculation, approximate mz and returning ROI$mzMin and ROI$mzMax for ROI #1\n", "Fit of ROI #3 is unsuccessful (try error)\n", "1 features to integrate with FIR\n", "Reading data from 1 windows\n")
# results (output, warnings and messages)
result_singleFileSearch <- evaluate_promise(peakPantheR_singleFileSearch(singleSpectraDataPath, tmp_ROI, peakStatistic=FALSE, plotEICsPath=NA, getAcquTime=FALSE, FIR=input_FIR, verbose=TRUE))
# Check results
expect_equal(result_singleFileSearch$result$TIC, expected_TIC)
expect_equal(result_singleFileSearch$result$peakTable, expected_peakTable, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$curveFit, expected_curveFit, tolerance=1e-6)
expect_equal(result_singleFileSearch$result$ROIsDataPoint, expected_ROIsDataPoint)
expect_equal(result_singleFileSearch$result$acquTime, expected_acquTime)
# Check messages (can't check timing)
expect_equal(length(result_singleFileSearch$messages), 11)
expect_equal(result_singleFileSearch$messages[c(1,2,4,5,7,8)], expected_messages)
})
test_that('raise errors', {
# paths to trigger errors
fakeInputPath <- './notAPath/test.CDF'
fakeOutputPath <- './notAPath/save.png'
wrongOutputFormat <- './notAPNG.txt'
# FIR to trigger errors
notADataFrame <- 'not at dataframe'
wrongNbrows <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(), c("mzMin", "mzMax", "rtMin", "rtMax"))), stringsAsFactors=FALSE)
wrongCols <- data.frame(matrix(vector(), 4, 4, dimnames=list(c(), c("wrongCol name", "mzMax", "rtMin", "rtMax"))), stringsAsFactors=FALSE)
# singleSpectraDataPath doesnt exist
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath=fakeInputPath, input_ROI), "Check input, file*")
# save folder doesnt exist
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, plotEICsPath=fakeOutputPath), "Check input, plotEICsPath folder*")
# save file is not a .png
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, plotEICsPath=wrongOutputFormat), "Check input, plotEICsPath file name*")
# not implemented curveModel
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, curveModel='FakeModel'), "Error: \"curveModel\" must be one of: skewedGaussian, emgGaussian")
# FIR is not a data.frame
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=notADataFrame), "Check input, FIR must be a data.frame not character")
# FIR has wrong number of rows
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=wrongNbrows), "Check input, FIR must have the same number of rows as targetFeatTable")
# FIR columns are wrong
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, input_ROI, FIR=wrongCols), 'Check input, FIR must have "mzMin", "mzMax", "rtMin" and "rtMax" as columns')
# rtMin > rtMax
wrong_ROI_rt <- input_ROI
wrong_ROI_rt[2,] <- c("ID-2", "testCpd 2", 3440., 3385.577, 3280., 496.195038, 496.2, 496.204962)
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, wrong_ROI_rt), 'Check input, "rtMin" must be <= to "rtMax"')
# mzMin > mzMax
wrong_ROI_mz <- input_ROI
wrong_ROI_mz[3,] <- c("ID-3", "testCpd 3", 3420., 3454.435, 3495., 464.204642, 464.2, 464.195358)
expect_error(peakPantheR_singleFileSearch(singleSpectraDataPath, wrong_ROI_mz), 'Check input, "mzMin" must be <= to "mzMax"')
})
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