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tests/testthat/test_peakPantheR_ROIStatistics.R
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments
context('peakPantheR_ROIStatistics()')
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
# 3 files
input_spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
system.file('cdf/KO/ko16.CDF', package = "faahKO"),
system.file('cdf/KO/ko18.CDF', package = "faahKO"))
# 4 features
input_targetFeatTable <- data.frame(matrix(vector(), 4, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_targetFeatTable[3,] <- c("ID-3", "Cpd 3", 3420., 3454.435, 3495., 464.195358, 464.2, 464.204642)
input_targetFeatTable[4,] <- c("ID-4", "Cpd 4", 3670., 3701.697, 3745., 536.194638, 536.2, 536.205362)
input_targetFeatTable[,c(3:8)] <- vapply(input_targetFeatTable[,c(3:8)], as.numeric, FUN.VALUE=numeric(4))
test_that('3 files, save EICS, mean IS RT, save IS fit, with sampleColour, verbose, no verbose', {
# temp saveFolder
saveFolder1 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder1, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# Expected save paths
expected_path_plot1 <- file.path(saveFolder1, "ID-1.png")
expected_path_plot2 <- file.path(saveFolder1, "ID-2.png")
expected_path_plot3 <- file.path(saveFolder1, "ID-3.png")
expected_path_plot4 <- file.path(saveFolder1, "ID-4.png")
expected_path_CSV <- file.path(saveFolder1, "IS_mean_RT.csv")
expected_path_IS_plot1 <- file.path(saveFolder1,"IS_search", "cpd_1.png")
expected_path_IS_plot2 <- file.path(saveFolder1,"IS_search", "cpd_2.png")
expected_path_IS_plot3 <- file.path(saveFolder1,"IS_search", "cpd_3.png")
expected_path_IS_plot4 <- file.path(saveFolder1,"IS_search", "cpd_4.png")
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- vapply(expected_meanIS[,2], as.numeric, FUN.VALUE=numeric(1))
# Expected message
expected_message <- c(" 4 ROI in 3 reference samples\n", " 4 IS in 3 reference samples\n", "\n-- Saving EICs for each ROI --\n","Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "----- ko15 -----\n", "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", "Annotation object cannot be reordered by sample acquisition date\n", "----------------\n", " 0 failure(s)\n", "Saving diagnostic plots:\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE))
# Check saved EIC plots
expect_true(file.exists(expected_path_plot1))
expect_true(file.exists(expected_path_plot2))
expect_true(file.exists(expected_path_plot3))
expect_true(file.exists(expected_path_plot4))
# Check saved IS fit
expect_true(file.exists(expected_path_IS_plot1))
expect_true(file.exists(expected_path_IS_plot2))
expect_true(file.exists(expected_path_IS_plot3))
expect_true(file.exists(expected_path_IS_plot4))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 64)
expect_equal(result_ROIstatsV$messages[c(2, 4:7, 9:10, 12:13, 16:23, 25:26, 54:55, 57, 59)], expected_message)
# no verbose
result_ROIstatsNoV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=FALSE))
expect_equal(length(result_ROIstatsNoV$messages), 6)
})
test_that('3 files (1 missing), save EICs, no IS RT, no IS fit, sampleColour is not of length nb spectra, verbose', {
# message for wrong sampleColour length
# temp saveFolder
saveFolder2 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder2, full.names=TRUE))))
# input
refSpecFiles <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
'not/a/valid/path',
system.file('cdf/KO/ko18.CDF', package = "faahKO"))
input_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green', 'yellow')
# Expected save paths
expected_path_plot1 <- file.path(saveFolder2, "ID-1.png")
expected_path_plot2 <- file.path(saveFolder2, "ID-2.png")
expected_path_plot3 <- file.path(saveFolder2, "ID-3.png")
expected_path_plot4 <- file.path(saveFolder2, "ID-4.png")
expected_path_CSV <- file.path(saveFolder2, "IS_mean_RT.csv")
# Expected message
expected_message <- c("Check input, \"sampleColour\" must be a vector of colour of same length as \"referenceSpectraFile\": default colour used instead\n", "No IS_ROI provided, mean RT of IS will not be calculated\n", " 4 ROI in 3 reference samples\n", "- Mean RT of IS will not be calculated\n", "\n-- Saving EICs for each ROI --\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder2, ROI=input_ROI, IS_ROI=NULL, sampleColour=sampleColour, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check saved EIC plots
expect_true(file.exists(expected_path_plot1))
expect_true(file.exists(expected_path_plot2))
expect_true(file.exists(expected_path_plot3))
expect_true(file.exists(expected_path_plot4))
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 14)
expect_equal(result_ROIstatsV$messages[c(1:2, 4:8)], expected_message)
})
test_that('3 files, no save EICs, mean IS RT, no IS fit, without sampleColour, verbose, no verbose', {
# temp saveFolder
saveFolder3 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder3, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
# Expected save paths
expected_path_CSV <- file.path(saveFolder3, "IS_mean_RT.csv")
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- vapply(expected_meanIS[,2], as.numeric, FUN.VALUE=numeric(1))
# Expected message
expected_message <- c("No ROI provided, EICs of ROI windows will not be saved\n", "- EICs of ROI windows will not be saved\n" , " 4 IS in 3 reference samples\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "----- ko15 -----\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Check input, mzMLPath must be a .mzML\n", "Reading data from 4 windows\n", "----------------\n", " 0 failure(s)\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder3, ROI=NULL, IS_ROI=input_IS_ROI, sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 47)
expect_equal(result_ROIstatsV$messages[c(1:2, 4:12, 44,46)], expected_message)
})
test_that('3 files, no save EICs (not a data.frame), no mean IS RT (not a data.frame), sampleColour is not character, verbose', {
# message for ROI not a data.frame, IS_ROI not a data.frame, sampleColour not a character
# temp saveFolder
saveFolder4 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder4, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- 'notADataframe'
input_IS_ROI <- 'notADataframe'
# Expected message
expected_message <- c("Check input, \"sampleColour\" must be a vector of colour of same length as \"referenceSpectraFile\": default colour used instead\n", "ROI is not a data.frame, EICs of ROI windows will not be saved\n", "IS_ROI is not a data.frame, mean RT of IS will not be calculated\n", "- EICs of ROI windows will not be saved\n", "- Mean RT of IS will not be calculated\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder4, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=42, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsV$messages), 5)
expect_equal(result_ROIstatsV$messages, expected_message)
})
test_that('3 files, no save EICs (wrong columns), no mean IS RT (wrong columns), verbose', {
# message for ROI and IS_ROI missing a column (cpdID, cpdName, rt, mz, rtMin, rtMax, mzMin, mzMax)
# temp saveFolder
saveFolder5 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder5, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
# Expected message
expected_message <- c("ROI columns must contain \"cpdID\", \"cpdName\", \"rtMin\", \"rt\", \"rtMax\", \"mzMin\", \"mz\" and \"mzMax\", EICs of ROI windows will not be saved\n", "IS_ROI columns must contain \"cpdID\", \"cpdName\", \"rtMin\", \"rt\", \"rtMax\", \"mzMin\", \"mz\" and \"mzMax\", mean RT of IS will not be calculated\n", "- EICs of ROI windows will not be saved\n", "- Mean RT of IS will not be calculated\n")
## no cpdID
# results (output, warnings and messages)
result_ROIstatsNoCpdID <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-1], IS_ROI=input_IS_ROI[,-1], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoCpdID$messages), 4)
expect_equal(result_ROIstatsNoCpdID$messages, expected_message)
## no cpdName
# results (output, warnings and messages)
result_ROIstatsNoCpdName <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-2], IS_ROI=input_IS_ROI[,-2], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoCpdName$messages), 4)
expect_equal(result_ROIstatsNoCpdName$messages, expected_message)
## no rtMin
# results (output, warnings and messages)
result_ROIstatsNoRtMin <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-3], IS_ROI=input_IS_ROI[,-3], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRtMin$messages), 4)
expect_equal(result_ROIstatsNoRtMin$messages, expected_message)
## no rt
# results (output, warnings and messages)
result_ROIstatsNoRt <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-4], IS_ROI=input_IS_ROI[,-4], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRt$messages), 4)
expect_equal(result_ROIstatsNoRt$messages, expected_message)
## no rtMax
# results (output, warnings and messages)
result_ROIstatsNoRtMax <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-5], IS_ROI=input_IS_ROI[,-5], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRtMax$messages), 4)
expect_equal(result_ROIstatsNoRtMax$messages, expected_message)
## no mzMin
# results (output, warnings and messages)
result_ROIstatsNoMzMin <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-6], IS_ROI=input_IS_ROI[,-6], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMzMin$messages), 4)
expect_equal(result_ROIstatsNoMzMin$messages, expected_message)
## no mz
# results (output, warnings and messages)
result_ROIstatsNoMz <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-7], IS_ROI=input_IS_ROI[,-7], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMz$messages), 4)
expect_equal(result_ROIstatsNoMz$messages, expected_message)
## no mzMax
# results (output, warnings and messages)
result_ROIstatsNoMzMax <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-8], IS_ROI=input_IS_ROI[,-8], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMzMax$messages), 4)
expect_equal(result_ROIstatsNoMzMax$messages, expected_message)
})
test_that('parallel give the same result: 3 files, no save EICs, mean IS RT, save IS fit, verbose', {
# temp saveFolder
saveFolder6 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder6, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- sapply(expected_meanIS[,2], as.numeric)
# Expected save paths
expected_path_CSV <- file.path(saveFolder6, "IS_mean_RT.csv")
expected_path_IS_plot1 <- file.path(saveFolder6,"IS_search", "cpd_1.png")
expected_path_IS_plot2 <- file.path(saveFolder6,"IS_search", "cpd_2.png")
expected_path_IS_plot3 <- file.path(saveFolder6,"IS_search", "cpd_3.png")
expected_path_IS_plot4 <- file.path(saveFolder6,"IS_search", "cpd_4.png")
# Expected message
expected_message_parallel <- c("No ROI provided, EICs of ROI windows will not be saved\n", "- EICs of ROI windows will not be saved\n", " 4 IS in 3 reference samples\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "Running 3 clusters of 1 files over 1 cores:\n", " starting cluster 1/3\n", " starting cluster 2/3\n", " starting cluster 3/3\n", "Annotation object cannot be reordered by sample acquisition date\n", "----------------\n", " 0 failure(s)\n", "All plots saved\n")
# results (output, warnings and messages)
result_ROIstats_parallel <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder6, ROI=NULL, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=1, saveISPlots=TRUE, verbose=TRUE))
# Check saved IS fit
expect_true(file.exists(expected_path_IS_plot1))
expect_true(file.exists(expected_path_IS_plot2))
expect_true(file.exists(expected_path_IS_plot3))
expect_true(file.exists(expected_path_IS_plot4))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstats_parallel$messages), 20)
expect_equal(result_ROIstats_parallel$messages[c(1,2,4:14,16,19)], expected_message_parallel)
})
test_that('raise errors', {
# temp saveFolder
saveFolder8 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder8, full.names=TRUE))))
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# referenceSpectraFiles is not a character vector
error_msg1 <- 'Check input, "referenceSpectraFiles" must be a vector of spectra paths'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=42, saveFolder8, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg1, fixed=TRUE)
# saveFolder is not a character
error_msg2 <- 'Check input, "saveFolder" must be a path'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=refSpecFiles, saveFolder=42 , ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg2, fixed=TRUE)
# saveFolder is not of length 1
error_msg3 <- 'Check input, "saveFolder" must be a path'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=refSpecFiles, saveFolder=c('onePath','anotherPath','morePath') , ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg3, fixed=TRUE)
})
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context('peakPantheR_ROIStatistics()')
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
# 3 files
input_spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
system.file('cdf/KO/ko16.CDF', package = "faahKO"),
system.file('cdf/KO/ko18.CDF', package = "faahKO"))
# 4 features
input_targetFeatTable <- data.frame(matrix(vector(), 4, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))),stringsAsFactors=FALSE)
input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222)
input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962)
input_targetFeatTable[3,] <- c("ID-3", "Cpd 3", 3420., 3454.435, 3495., 464.195358, 464.2, 464.204642)
input_targetFeatTable[4,] <- c("ID-4", "Cpd 4", 3670., 3701.697, 3745., 536.194638, 536.2, 536.205362)
input_targetFeatTable[,c(3:8)] <- vapply(input_targetFeatTable[,c(3:8)], as.numeric, FUN.VALUE=numeric(4))
test_that('3 files, save EICS, mean IS RT, save IS fit, with sampleColour, verbose, no verbose', {
# temp saveFolder
saveFolder1 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder1, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# Expected save paths
expected_path_plot1 <- file.path(saveFolder1, "ID-1.png")
expected_path_plot2 <- file.path(saveFolder1, "ID-2.png")
expected_path_plot3 <- file.path(saveFolder1, "ID-3.png")
expected_path_plot4 <- file.path(saveFolder1, "ID-4.png")
expected_path_CSV <- file.path(saveFolder1, "IS_mean_RT.csv")
expected_path_IS_plot1 <- file.path(saveFolder1,"IS_search", "cpd_1.png")
expected_path_IS_plot2 <- file.path(saveFolder1,"IS_search", "cpd_2.png")
expected_path_IS_plot3 <- file.path(saveFolder1,"IS_search", "cpd_3.png")
expected_path_IS_plot4 <- file.path(saveFolder1,"IS_search", "cpd_4.png")
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- vapply(expected_meanIS[,2], as.numeric, FUN.VALUE=numeric(1))
# Expected message
expected_message <- c(" 4 ROI in 3 reference samples\n", " 4 IS in 3 reference samples\n", "\n-- Saving EICs for each ROI --\n","Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "----- ko15 -----\n", "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$mzMax for ROI #3\n", "Annotation object cannot be reordered by sample acquisition date\n", "----------------\n", " 0 failure(s)\n", "Saving diagnostic plots:\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE))
# Check saved EIC plots
expect_true(file.exists(expected_path_plot1))
expect_true(file.exists(expected_path_plot2))
expect_true(file.exists(expected_path_plot3))
expect_true(file.exists(expected_path_plot4))
# Check saved IS fit
expect_true(file.exists(expected_path_IS_plot1))
expect_true(file.exists(expected_path_IS_plot2))
expect_true(file.exists(expected_path_IS_plot3))
expect_true(file.exists(expected_path_IS_plot4))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 64)
expect_equal(result_ROIstatsV$messages[c(2, 4:7, 9:10, 12:13, 16:23, 25:26, 54:55, 57, 59)], expected_message)
# no verbose
result_ROIstatsNoV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder1, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=FALSE))
expect_equal(length(result_ROIstatsNoV$messages), 6)
})
test_that('3 files (1 missing), save EICs, no IS RT, no IS fit, sampleColour is not of length nb spectra, verbose', {
# message for wrong sampleColour length
# temp saveFolder
saveFolder2 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder2, full.names=TRUE))))
# input
refSpecFiles <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
'not/a/valid/path',
system.file('cdf/KO/ko18.CDF', package = "faahKO"))
input_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green', 'yellow')
# Expected save paths
expected_path_plot1 <- file.path(saveFolder2, "ID-1.png")
expected_path_plot2 <- file.path(saveFolder2, "ID-2.png")
expected_path_plot3 <- file.path(saveFolder2, "ID-3.png")
expected_path_plot4 <- file.path(saveFolder2, "ID-4.png")
expected_path_CSV <- file.path(saveFolder2, "IS_mean_RT.csv")
# Expected message
expected_message <- c("Check input, \"sampleColour\" must be a vector of colour of same length as \"referenceSpectraFile\": default colour used instead\n", "No IS_ROI provided, mean RT of IS will not be calculated\n", " 4 ROI in 3 reference samples\n", "- Mean RT of IS will not be calculated\n", "\n-- Saving EICs for each ROI --\n", "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.\n", "Reading data from 4 windows\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder2, ROI=input_ROI, IS_ROI=NULL, sampleColour=sampleColour, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check saved EIC plots
expect_true(file.exists(expected_path_plot1))
expect_true(file.exists(expected_path_plot2))
expect_true(file.exists(expected_path_plot3))
expect_true(file.exists(expected_path_plot4))
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 14)
expect_equal(result_ROIstatsV$messages[c(1:2, 4:8)], expected_message)
})
test_that('3 files, no save EICs, mean IS RT, no IS fit, without sampleColour, verbose, no verbose', {
# temp saveFolder
saveFolder3 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder3, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
# Expected save paths
expected_path_CSV <- file.path(saveFolder3, "IS_mean_RT.csv")
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- vapply(expected_meanIS[,2], as.numeric, FUN.VALUE=numeric(1))
# Expected message
expected_message <- c("No ROI provided, EICs of ROI windows will not be saved\n", "- EICs of ROI windows will not be saved\n" , " 4 IS in 3 reference samples\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "----- ko15 -----\n", "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", "----------------\n", " 0 failure(s)\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder3, ROI=NULL, IS_ROI=input_IS_ROI, sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstatsV$messages), 47)
expect_equal(result_ROIstatsV$messages[c(1:2, 4:12, 44,46)], expected_message)
})
test_that('3 files, no save EICs (not a data.frame), no mean IS RT (not a data.frame), sampleColour is not character, verbose', {
# message for ROI not a data.frame, IS_ROI not a data.frame, sampleColour not a character
# temp saveFolder
saveFolder4 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder4, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- 'notADataframe'
input_IS_ROI <- 'notADataframe'
# Expected message
expected_message <- c("Check input, \"sampleColour\" must be a vector of colour of same length as \"referenceSpectraFile\": default colour used instead\n", "ROI is not a data.frame, EICs of ROI windows will not be saved\n", "IS_ROI is not a data.frame, mean RT of IS will not be calculated\n", "- EICs of ROI windows will not be saved\n", "- Mean RT of IS will not be calculated\n")
# results (output, warnings and messages)
result_ROIstatsV <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder4, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=42, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsV$messages), 5)
expect_equal(result_ROIstatsV$messages, expected_message)
})
test_that('3 files, no save EICs (wrong columns), no mean IS RT (wrong columns), verbose', {
# message for ROI and IS_ROI missing a column (cpdID, cpdName, rt, mz, rtMin, rtMax, mzMin, mzMax)
# temp saveFolder
saveFolder5 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder5, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
# Expected message
expected_message <- c("ROI columns must contain \"cpdID\", \"cpdName\", \"rtMin\", \"rt\", \"rtMax\", \"mzMin\", \"mz\" and \"mzMax\", EICs of ROI windows will not be saved\n", "IS_ROI columns must contain \"cpdID\", \"cpdName\", \"rtMin\", \"rt\", \"rtMax\", \"mzMin\", \"mz\" and \"mzMax\", mean RT of IS will not be calculated\n", "- EICs of ROI windows will not be saved\n", "- Mean RT of IS will not be calculated\n")
## no cpdID
# results (output, warnings and messages)
result_ROIstatsNoCpdID <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-1], IS_ROI=input_IS_ROI[,-1], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoCpdID$messages), 4)
expect_equal(result_ROIstatsNoCpdID$messages, expected_message)
## no cpdName
# results (output, warnings and messages)
result_ROIstatsNoCpdName <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-2], IS_ROI=input_IS_ROI[,-2], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoCpdName$messages), 4)
expect_equal(result_ROIstatsNoCpdName$messages, expected_message)
## no rtMin
# results (output, warnings and messages)
result_ROIstatsNoRtMin <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-3], IS_ROI=input_IS_ROI[,-3], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRtMin$messages), 4)
expect_equal(result_ROIstatsNoRtMin$messages, expected_message)
## no rt
# results (output, warnings and messages)
result_ROIstatsNoRt <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-4], IS_ROI=input_IS_ROI[,-4], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRt$messages), 4)
expect_equal(result_ROIstatsNoRt$messages, expected_message)
## no rtMax
# results (output, warnings and messages)
result_ROIstatsNoRtMax <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-5], IS_ROI=input_IS_ROI[,-5], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoRtMax$messages), 4)
expect_equal(result_ROIstatsNoRtMax$messages, expected_message)
## no mzMin
# results (output, warnings and messages)
result_ROIstatsNoMzMin <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-6], IS_ROI=input_IS_ROI[,-6], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMzMin$messages), 4)
expect_equal(result_ROIstatsNoMzMin$messages, expected_message)
## no mz
# results (output, warnings and messages)
result_ROIstatsNoMz <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-7], IS_ROI=input_IS_ROI[,-7], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMz$messages), 4)
expect_equal(result_ROIstatsNoMz$messages, expected_message)
## no mzMax
# results (output, warnings and messages)
result_ROIstatsNoMzMax <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder5, ROI=input_ROI[,-8], IS_ROI=input_IS_ROI[,-8], sampleColour=NULL, ncores=0, saveISPlots=FALSE, verbose=TRUE))
# Check messages
expect_equal(length(result_ROIstatsNoMzMax$messages), 4)
expect_equal(result_ROIstatsNoMzMax$messages, expected_message)
})
test_that('parallel give the same result: 3 files, no save EICs, mean IS RT, save IS fit, verbose', {
# temp saveFolder
saveFolder6 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder6, full.names=TRUE))))
# input
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# Expected IS mean RT
expected_meanIS <- data.frame(matrix(nrow=4,ncol=2,dimnames=list(c(), c('X','mean_rt'))))
expected_meanIS[1,] <- c('ID-1', 3360.054253)
expected_meanIS[2,] <- c('ID-2', 3401.938353)
expected_meanIS[3,] <- c('ID-3', 3458.840343)
expected_meanIS[4,] <- c('ID-4', 3712.859261)
expected_meanIS[,2] <- sapply(expected_meanIS[,2], as.numeric)
# Expected save paths
expected_path_CSV <- file.path(saveFolder6, "IS_mean_RT.csv")
expected_path_IS_plot1 <- file.path(saveFolder6,"IS_search", "cpd_1.png")
expected_path_IS_plot2 <- file.path(saveFolder6,"IS_search", "cpd_2.png")
expected_path_IS_plot3 <- file.path(saveFolder6,"IS_search", "cpd_3.png")
expected_path_IS_plot4 <- file.path(saveFolder6,"IS_search", "cpd_4.png")
# Expected message
expected_message_parallel <- c("No ROI provided, EICs of ROI windows will not be saved\n", "- EICs of ROI windows will not be saved\n", " 4 IS in 3 reference samples\n", "\n-- Calculating mean RT for each IS --\n", "Processing 4 compounds in 3 samples:\n", " uROI:\tFALSE\n", " FIR:\tFALSE\n", "Running 3 clusters of 1 files over 1 cores:\n", " starting cluster 1/3\n", " starting cluster 2/3\n", " starting cluster 3/3\n", "Annotation object cannot be reordered by sample acquisition date\n", "----------------\n", " 0 failure(s)\n", "All plots saved\n")
# results (output, warnings and messages)
result_ROIstats_parallel <- evaluate_promise(peakPantheR_ROIStatistics(refSpecFiles, saveFolder6, ROI=NULL, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=1, saveISPlots=TRUE, verbose=TRUE))
# Check saved IS fit
expect_true(file.exists(expected_path_IS_plot1))
expect_true(file.exists(expected_path_IS_plot2))
expect_true(file.exists(expected_path_IS_plot3))
expect_true(file.exists(expected_path_IS_plot4))
# Check mean IS RT
expect_true(file.exists(expected_path_CSV))
saved_CSV <- read.csv(expected_path_CSV, header=TRUE, sep=",", quote="\"", stringsAsFactors=FALSE)
expect_equal(saved_CSV, expected_meanIS, tolerance=1e-4)
# Check messages (no filepaths)
expect_equal(length(result_ROIstats_parallel$messages), 20)
expect_equal(result_ROIstats_parallel$messages[c(1,2,4:14,16,19)], expected_message_parallel)
})
test_that('raise errors', {
# temp saveFolder
saveFolder8 <- tempdir()
# clear temp folder
suppressWarnings(do.call(file.remove, list(list.files(saveFolder8, full.names=TRUE))))
refSpecFiles <- input_spectraPaths
input_ROI <- input_targetFeatTable
input_IS_ROI <- input_targetFeatTable
sampleColour <- c('blue', 'red', 'green')
# referenceSpectraFiles is not a character vector
error_msg1 <- 'Check input, "referenceSpectraFiles" must be a vector of spectra paths'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=42, saveFolder8, ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg1, fixed=TRUE)
# saveFolder is not a character
error_msg2 <- 'Check input, "saveFolder" must be a path'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=refSpecFiles, saveFolder=42 , ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg2, fixed=TRUE)
# saveFolder is not of length 1
error_msg3 <- 'Check input, "saveFolder" must be a path'
expect_error(peakPantheR_ROIStatistics(referenceSpectraFiles=refSpecFiles, saveFolder=c('onePath','anotherPath','morePath') , ROI=input_ROI, IS_ROI=input_IS_ROI, sampleColour=sampleColour, ncores=0, saveISPlots=TRUE, verbose=TRUE), error_msg3, fixed=TRUE)
})
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