/
project-tool.R
1631 lines (1498 loc) · 78.1 KB
/
project-tool.R
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#' @include main.R
NULL
getScriptCode <- function(input, analyses)
{
txtCon <- withr::local_connection(textConnection(NULL, "w"))
# helper functions
doQuote <- function(txt) paste0("\"", txt, "\"")
addText <- function(txt) writeLines(txt, txtCon)
addNL <- function(count = 1) addText(rep("", count))
addComment <- function(txt, condition = TRUE) { if (condition) addText(paste("#", txt)) }
addHeader <- function(title)
{
hd <- strrep("-", 25)
addNL()
addComment(c(hd, title, hd))
addNL()
}
addAssignment <- function(var, val, quote = FALSE) addText(paste(var, "<-", if (quote) doQuote(val) else val))
addCall <- function(var, func, args, condition = TRUE, indent = 0)
{
if (!condition)
return(NULL)
if (!is.list(args[[1]]))
args <- list(args) # HACK: allow unnested lists for cases with one arg
args <- lapply(args, function(a)
{
# handle args
# - add names if necessary
# - handle conditional args
# - handle strings
# - handle conditional NULLs
if (!is.null(a[["condition"]]) && !a$condition)
return(NULL)
ret <- a$value
if (is.null(a[["value"]]) || (!is.null(a[["isNULL"]]) && a$isNULL) ||
(!is.null(a[["zeroToNULL"]]) && a$zeroToNULL && a$value == 0))
ret <- "NULL"
else if (!is.null(a[["quote"]]) && a$quote)
ret <- doQuote(ret)
if (length(ret) > 1)
ret <- paste0("c(", paste0(ret, collapse = ", "), ")")
if (!is.null(a[["name"]]))
ret <- paste(a$name, "=", ret)
return(ret)
})
args <- pruneList(args)
argText <- paste0(args, collapse = ", ")
callPrefix <- paste0(strrep(" ", indent), if (!is.null(var)) paste0(var, " <- ") else "", func, "(")
singleLineLength <- nchar(callPrefix) + nchar(argText) + nchar(")")
if (singleLineLength > 120)
{
# HACK: temporary replace " = " with "|=|" in order to keep var assignments on the same line
args <- lapply(args, function(a)
{
a <- gsub(", ", ",|", a, fixed = TRUE) # items in a list
a <- gsub(" = ", "|=|", a, fixed = TRUE) # named arg assignments
return(a)
})
argText <- paste0(args, collapse = ", ")
argText <- paste0(strwrap(argText, 120 - nchar(callPrefix) - 1, # -1: trailing ")"
exdent = nchar(callPrefix)),
collapse = "\n")
argText <- gsub("|", " ", argText, fixed = TRUE)
}
cl <- paste0(callPrefix, argText, ")")
addText(cl)
}
addAnaInfo <- function(anaInfoVarName, anaTable, anaTableFile, comment, ionization)
{
if (input$generateAnaInfo == "table")
{
addComment("Load analysis table", condition = comment)
addCall(anaInfoVarName, "read.csv", list(value = anaTableFile, quote = TRUE))
}
else if (input$generateAnaInfo == "script")
{
addCall(anaInfoVarName, "generateAnalysisInfo", list(
list(name = "paths", value = unique(anaTable$path), quote = TRUE),
list(name = "groups", value = anaTable$group, quote = TRUE),
list(name = "blanks", value = anaTable$blank, quote = TRUE),
list(name = "concs", value = anaTable$conc),
list(name = "norm_concs", value = anaTable$norm_conc)
))
if (any(anaTable$exclude))
{
toExclude <- paste0('c(', paste0(which(anaTable$exclude), collapse = ', '), ')')
addAssignment(anaInfoVarName, paste0(anaInfoVarName, '[-', toExclude, ', ]'))
addNL()
}
}
else if (input$generateAnaInfo == "example")
{
addComment("Example data from patRoonData package (triplicate solvent blank + triplicate standard)",
condition = comment)
addCall(anaInfoVarName, "patRoonData::exampleAnalysisInfo", list(value = ionization, quote = TRUE))
}
else # none
{
addComment("NOTE: please set anaInfo to a valid data.frame with analysis information. See ?`analysis-information` for more details.",
condition = comment)
addCall(anaInfoVarName, "data.frame", list(
list(name = "path", value = "character()"),
list(name = "analysis", value = "character()"),
list(name = "groups", value = "character()"),
list(name = "blanks", value = "character()")
))
}
}
addPrepBlock <- function(anaInfoVarName, DAMethodVarName)
{
addCall(NULL, "setDAMethod", list(
list(value = anaInfoVarName),
list(value = input[[DAMethodVarName]], quote = TRUE)
), condition = nzchar(input[[DAMethodVarName]]), indent = 4)
addCall(NULL, "recalibrarateDAFiles", list(value = anaInfoVarName), condition = input$doDACalib, indent = 4)
if (nzchar(input$convAlgo))
{
if (input$peakPicking)
centroid <- if (input$peakPickingVendor && input$convAlgo == "pwiz") "\"vendor\"" else TRUE
else
centroid <- FALSE
for (of in input$convTo)
{
addCall(NULL, "convertMSFiles", list(
list(name = "anaInfo", value = anaInfoVarName),
list(name = "from", value = input$convFrom, quote = TRUE),
list(name = "to", value = of, quote = TRUE),
list(name = "algorithm", value = input$convAlgo, quote = TRUE),
list(name = "centroid", value = centroid)),
indent = 4)
}
}
}
addFindFeatures <- function(varName, anaInfoVarName)
{
addCall(varName, "findFeatures", list(
list(value = anaInfoVarName),
list(value = if (input$featFinder == "XCMS") "xcms3" else tolower(input$featFinder), quote = TRUE),
list(name = "noiseThrInt", value = 1000, condition = input$featFinder == "OpenMS"),
list(name = "chromSNR", value = 3, condition = input$featFinder == "OpenMS"),
list(name = "chromFWHM", value = 5, condition = input$featFinder == "OpenMS"),
list(name = "minFWHM", value = 1, condition = input$featFinder == "OpenMS"),
list(name = "maxFWHM", value = 30, condition = input$featFinder == "OpenMS"),
list(name = "kmeans", value = TRUE, condition = input$featFinder == "KPIC2"),
list(name = "level", value = 1000, condition = input$featFinder == "KPIC2"),
list(name = "doFMF", value = TRUE, condition = input$featFinder == "Bruker")
))
}
getAdductArg <- function(cond = TRUE) list(name = "adduct", value = if (input$ionization == "positive") "[M+H]+" else "[M-H]-",
quote = TRUE,
condition = input$ionization != "both" &&
(!nzchar(input$components) || input$components == "nontarget" || !input$selectIons) &&
cond)
addLoadSuspCall <- function(var, file)
{
addCall(var, "read.csv", list(
list(value = file, quote = TRUE),
list(name = "stringsAsFactors", value = FALSE)
))
}
addLoadSuspList <- function(name, doEx, varBase, exVarBase, inpVarBase)
{
# Generalized for suspect screening and ISTD normalization
varBasePos <- paste0(varBase, "Pos"); varBaseNeg <- paste0(varBase, "Neg")
if (doEx)
{
addComment(paste("Get example", name))
exVarBasePos <- paste0("patRoonData::", exVarBase, "Pos")
exVarBaseNeg <- paste0("patRoonData::", exVarBase, "Neg")
if (input$ionization == "positive")
addAssignment(varBase, exVarBasePos)
else if (input$ionization == "negative")
addAssignment(varBase, exVarBaseNeg)
else
{
addAssignment(varBasePos, exVarBasePos)
addAssignment(varBaseNeg, exVarBaseNeg)
}
}
else
{
addComment(paste("Load", name))
if (input$ionization != "both")
addLoadSuspCall(varBase, input[[inpVarBase]])
else
{
if (nzchar(input$suspectListNeg))
{
addLoadSuspCall(varBasePos, input[[paste0(inpVarBase, "Pos")]])
addLoadSuspCall(varBaseNeg, input[[paste0(inpVarBase, "Neg")]])
}
else
addLoadSuspCall(varBase, input[[paste0(inpVarBase, "Pos")]])
}
}
}
addScreenCall <- function(susp, oh = TRUE, am = NULL)
{
addCall("fGroups", "screenSuspects", list(
list(value = "fGroups"),
list(value = susp),
list(name = "rtWindow", value = 12),
list(name = "mzWindow", value = 0.005),
getAdductArg(),
list(name = "onlyHits", value = oh),
list(name = "amend", value = am, condition = !is.null(am))
))
}
addComment(paste("Script automatically generated on", date()))
addNL()
addCall(NULL, "library", list(value = "patRoon"))
addHeader("initialization")
addAssignment("workPath", input$destinationPath, quote = TRUE)
addCall(NULL, "setwd", list(value = "workPath"))
addNL()
if (input$ionization != "both")
addAnaInfo("anaInfo", analyses, input$analysisTableFile, TRUE, input$ionization)
else
{
addAnaInfo("anaInfoPos", analyses$pos, input$analysisTableFilePos, TRUE, "positive")
addAnaInfo("anaInfoNeg", analyses$neg, input$analysisTableFileNeg, FALSE, "negative")
}
if (nzchar(input$convAlgo) || nzchar(input$DAMethod) || input$doDACalib)
{
addNL()
addComment("Set to FALSE to skip data pre-treatment")
addAssignment("doDataPretreatment", TRUE)
addText("if (doDataPretreatment)\n{")
if (input$ionization != "both")
addPrepBlock("anaInfo", "DAMethod")
else
{
addPrepBlock("anaInfoPos", "DAMethodPos")
addNL()
addPrepBlock("anaInfoNeg", "DAMethodNeg")
}
addText("}")
}
addHeader("features")
if (input$featGrouper != "SIRIUS") # NOTE: never the case with sets
{
addComment("Find all features")
addComment(sprintf("NOTE: see the %s manual for many more options",
if (input$featFinder == "OpenMS") "reference" else input$featFinder),
condition = !input$featFinder %in% c("Bruker", "SIRIUS"))
if (input$ionization != "both")
addFindFeatures("fList", "anaInfo")
else
{
addFindFeatures("fListPos", "anaInfoPos")
addFindFeatures("fListNeg", "anaInfoNeg")
addCall("fList", "makeSet", list(
list(value = "fListPos"),
list(value = "fListNeg"),
list(name = "adducts", value = c("[M+H]+", "[M-H]-"), quote = TRUE)
))
}
addNL()
}
addComment("Group and align features between analyses")
addCall("fGroups", "groupFeatures", list(
list(value = "fList", condition = input$featGrouper != "SIRIUS"),
list(value = "anaInfo", condition = input$featGrouper == "SIRIUS"),
list(value = if (input$featGrouper == "XCMS") "xcms3" else tolower(input$featGrouper), quote = TRUE),
list(name = "rtalign", value = TRUE, condition = input$featGrouper != "SIRIUS"),
list(name = "groupParam", value = "xcms::PeakDensityParam(sampleGroups = analysisInfo(fList)$group)",
condition = input$featGrouper == "XCMS"),
list(name = "retAlignParam", value = "xcms::ObiwarpParam()", condition = input$featGrouper == "XCMS")
))
retRange <- c(input[["retention-min"]], input[["retention-max"]])
if (all(retRange == 0))
retRange <- NULL
else if (retRange[2] == 0)
retRange[2] <- Inf
mzRange <- c(input[["mz-min"]], input[["mz-max"]])
if (all(mzRange == 0))
mzRange <- NULL
else if (mzRange[2] == 0)
mzRange[2] <- Inf
addNL()
addComment("Basic rule based filtering")
addCall("fGroups", "filter", list(
list(value = "fGroups"),
list(name = "preAbsMinIntensity", value = input$preIntThr, zeroToNULL = TRUE),
list(name = "absMinIntensity", value = input$intThr, zeroToNULL = TRUE),
list(name = "relMinReplicateAbundance", value = input$repAbundance, zeroToNULL = TRUE),
list(name = "maxReplicateIntRSD", value = input$maxRepRSD, zeroToNULL = TRUE),
list(name = "blankThreshold", value = input$blankThr, zeroToNULL = TRUE),
list(name = "removeBlanks", value = input$removeBlanks),
list(name = "retentionRange", value = retRange),
list(name = "mzRange", value = mzRange)
))
if (nzchar(input$components))
{
addHeader("componentization")
addComment("Perform automatic generation of components")
addCall("components", "generateComponents", list(
list(value = "fGroups"),
list(value = tolower(input$components), quote = TRUE),
list(name = "ionization", value = input$ionization, quote = TRUE, condition = input$ionization != "both"),
list(name = "rtRange", value = c(-120, 120), condition = input$components == "nontarget"),
list(name = "mzRange", value = c(5, 120), condition = input$components == "nontarget"),
list(name = "elements", value = c("C", "H", "O"), quote = TRUE, condition = input$components == "nontarget"),
list(name = "rtDev", value = 30, condition = input$components == "nontarget"),
list(name = "absMzDev", value = 0.002, condition = input$components == "nontarget")
))
if (input$selectIons && input$components != "nontarget")
{
pa <- switch(input$ionization,
positive = "[M+H]+",
negative = "[M-H]-",
both = c("[M+H]+", "[M-H]-"))
addCall("fGroups", "selectIons", list(
list(value = "fGroups"),
list(value = "components"),
list(name = "prefAdduct", value = pa, quote = TRUE),
list(name = "onlyMonoIso", value = TRUE)
))
}
}
if (input$featNorm != "none" || input$groupNorm)
{
addHeader("normalization")
if (input$featNorm == "istd")
{
addLoadSuspList("ISTD list",
(input$ionization != "both" && !nzchar(input$ISTDList)) ||
(input$ionization == "both" && !nzchar(input$ISTDListPos)),
"ISTDList", "ISTDList", "ISTDList")
addNL()
if (input$ionization != "both")
addComment("Set adduct to NULL if ISTD list contains an adduct column")
standards <- if (input$ionization != "both" || (!input$exSuspList && !nzchar(input$suspectListNeg)))
"ISTDList"
else
c("ISTDListPos", "ISTDListNeg")
}
else
standards <- NULL
addCall("fGroups", "normInts", list(
list(value = "fGroups"),
list(name = "featNorm", value = input$featNorm, quote = TRUE),
list(name = "groupNorm", value = input$groupNorm),
list(name = "normFunc", value = "max"),
list(name = "standards", value = standards, condition = input$featNorm == "istd"),
list(name = "ISTDRTWindow", value = 120, condition = input$featNorm == "istd"),
list(name = "ISTDMZWindow", value = 300, condition = input$featNorm == "istd"),
list(name = "minISTDs", value = 3, condition = input$featNorm == "istd"),
list(name = "rtWindow", value = 12, condition = input$featNorm == "istd"),
list(name = "mzWindow", value = 0.005, condition = input$featNorm == "istd"),
getAdductArg(input$featNorm == "istd")
))
}
doSusps <- input$exSuspList || (input$ionization != "both" && nzchar(input$suspectList)) ||
(input$ionization == "both" && nzchar(input$suspectListPos))
if (doSusps)
{
addHeader("suspect screening")
addLoadSuspList("suspect list", input$exSuspList, "suspList", "suspects", "suspectList")
useScrForTPScreening <- input$doTPs && input$TPGen != "Logic" && input$TPGenInput == "screening"
addNL()
if (useScrForTPScreening)
addComment("NOTE: onlyHits is set to FALSE to ensure TPs can be found below")
else
addComment("Set onlyHits to FALSE to retain features without suspects (eg for full NTA)")
if (input$ionization != "both")
addComment("Set adduct to NULL if suspect list contains an adduct column")
if (input$ionization != "both" || (!input$exSuspList && !nzchar(input$suspectListNeg)))
addScreenCall("suspList", !useScrForTPScreening)
else
addScreenCall("list(suspListPos, suspListNeg)", !useScrForTPScreening)
}
else
useScrForTPScreening <- FALSE
if (input$doTPs)
{
addHeader("transformation products")
if (input$TPGen != "Logic" && input$TPGenInput == "suspects")
{
addComment("Load parent suspect list")
addLoadSuspCall("suspListParents", input$TPSuspectList)
addNL()
}
addComment("Obtain TPs")
addCall("TPs", "generateTPs", list(
list(value = tolower(input$TPGen), quote = TRUE),
list(name = "parents", value = switch(input$TPGenInput,
suspects = "suspListParents",
screening = "fGroups",
all = "NULL"),
condition = input$TPGen != "Logic"),
list(value = "fGroups", condition = input$TPGen == "Logic"),
getAdductArg(input$TPGen == "Logic"),
list(name = "type", value = "env", quote = TRUE, condition = input$TPGen == "BioTransformer"),
list(name = "transLibrary", value = "photolysis_ranked", quote = TRUE, condition = input$TPGen == "CTS"),
list(name = "generations", value = if (input$TPGen == "BioTransformer") 2 else 1,
condition = input$TPGen != "Logic"),
list(name = "calcSims", value = FALSE, condition = input$TPGen != "Logic")
))
addNL()
addComment("Screen TPs")
addCall("suspListTPs", "convertToSuspects", list(
list(value = "TPs"),
list(name = "includeParents", value = FALSE)
))
if (useScrForTPScreening)
addComment("Amend with TP screening")
addScreenCall("suspListTPs", am = if (useScrForTPScreening) TRUE else NULL)
}
doMSPL <- nzchar(input$formulaGen) || nzchar(input$compIdent)
if (nzchar(input$formulaGen) || nzchar(input$compIdent))
{
addHeader("annotation")
useFMF <- input$featFinder == "Bruker" && input$peakListGen == "Bruker"
addComment("Retrieve MS peak lists")
addCall("avgMSListParams", "getDefAvgPListParams", list(name = "clusterMzWindow", value = 0.005))
addCall("mslists", "generateMSPeakLists", list(
list(value = "fGroups"),
list(value = "mzr", quote = TRUE, condition = input$peakListGen == "mzR"),
list(value = if (useFMF) "brukerfmf" else "bruker", quote = TRUE, condition = input$peakListGen == "Bruker"),
list(name = "maxMSRtWindow", value = 5, condition = !useFMF),
list(name = "precursorMzWindow", value = if (input$DIA) "NULL" else input$precursorMzWindow,
input$peakListGen == "mzR"),
list(name = "bgsubtr", value = TRUE, condition = !useFMF && input$peakListGen == "Bruker"),
list(name = "MSMSType", value = if (input$DIA) "BBCID" else "MSMS", quote = TRUE,
condition = !useFMF && input$peakListGen == "Bruker"),
list(name = "avgFeatParams", value = "avgMSListParams", condition = input$peakListGen == "mzR"),
list(name = "avgFGroupParams", value = "avgMSListParams")
))
addComment("Rule based filtering of MS peak lists. You may want to tweak this. See the manual for more information.")
addCall("mslists", "filter", list(
list(value = "mslists"),
list(name = "absMSIntThr", value = "NULL"),
list(name = "absMSMSIntThr", value = "NULL"),
list(name = "relMSIntThr", value = "NULL"),
list(name = "relMSMSIntThr", value = 0.05),
list(name = "topMSPeaks", value = "NULL"),
list(name = "topMSMSPeaks", value = 25)
))
if (nzchar(input$formulaGen))
{
addNL()
addComment("Calculate formula candidates")
addCall("formulas", "generateFormulas", list(
list(value = "fGroups"),
list(value = "mslists"),
list(value = tolower(input$formulaGen), quote = TRUE),
list(name = "relMzDev", value = 5, condition = input$formulaGen != "Bruker"),
list(name = "precursorMzSearchWindow", value = 0.002, condition = input$formulaGen == "Bruker"),
getAdductArg(),
list(name = "elements", value = "CHNOP", quote = TRUE, condition = input$formulaGen != "Bruker"),
list(name = "oc", value = FALSE, condition = input$formulaGen == "GenForm"),
list(name = "profile", value = "qtof", quote = TRUE, condition = input$formulaGen == "SIRIUS"),
list(name = "calculateFeatures", value = "TRUE", condition = input$formulaGen != "Bruker"),
list(name = "featThresholdAnn", value = 0.75),
list(name = "setThresholdAnn", value = 0, condition = input$ionization == "both")
))
}
if (nzchar(input$compIdent))
{
addNL()
if (input$compIdent == "Library")
{
addComment("Load MS library. You may want to filter it, please see the manuals for more details.")
addCall("mslibrary", "loadMSLibrary", list(
list(value = input$MSLibraryPath, quote = TRUE),
list(value = input$MSLibraryFormat, quote = TRUE),
list(name = "absMzDev", value = 0.002)
))
}
doTPDB <- input$compIdent == "MetFrag" && input$doTPs && input$TPGen != "Logic" && input$TPDoMFDB
if (doTPDB)
addCall(NULL, "convertToMFDB", list(
list(value = "TPs"),
list(value = "TP-database.csv", quote = TRUE),
list(name = "includeParents", value = TRUE)))
addComment("Calculate compound structure candidates")
if (input$compIdent == "SIRIUS")
{
addComment("If you are using SIRIUS 5 you need to be logged in to use CSI:FingerID to obtain structure candidates.")
addAssignment("tokenFID", "NULL")
addComment("Uncomment the following line to get the refresh token to log in (only need to obtain it once).")
addCall("# tokenFID", "getSIRIUSToken", list(value = "my@mail.com", quote = TRUE))
}
addCall("compounds", "generateCompounds", list(
list(value = "fGroups"),
list(value = "mslists"),
list(value = tolower(input$compIdent), quote = TRUE),
list(name = "dbRelMzDev", value = 5, condition = input$compIdent == "MetFrag"),
list(name = "fragRelMzDev", value = 5, condition = input$compIdent == "MetFrag"),
list(name = "fragAbsMzDev", value = 0.002, condition = input$compIdent == "MetFrag"),
list(name = "relMzDev", value = 5, condition = input$compIdent == "SIRIUS"),
getAdductArg(),
list(name = "database", value = "pubchem", quote = TRUE, condition = input$compIdent == "MetFrag" && !doTPDB),
list(name = "database", value = "csv", quote = TRUE, condition = doTPDB),
list(name = "extraOpts", value = "list(LocalDatabasePath = \"TP-database.csv\")", condition = doTPDB),
list(name = "maxCandidatesToStop", value = 2500, condition = input$compIdent == "MetFrag"),
list(name = "fingerIDDatabase", value = "pubchem", quote = TRUE, condition = input$compIdent == "SIRIUS"),
list(name = "elements", value = "CHNOP", quote = TRUE, condition = input$compIdent == "SIRIUS"),
list(name = "profile", value = "qtof", quote = TRUE, condition = input$compIdent == "SIRIUS"),
list(name = "token", value = "tokenFID", condition = input$compIdent == "SIRIUS"),
list(name = "MSLibrary", value = "mslibrary", condition = input$compIdent == "Library"),
list(name = "minSim", value = 0.75, condition = input$compIdent == "Library"),
list(name = "absMzDev", value = 0.002, condition = input$compIdent == "Library"),
list(name = "specSimParams", value = "getDefSpecSimParams()", condition = input$compIdent == "Library"),
list(name = "setThresholdAnn", value = 0, condition = input$ionization == "both")
))
if (input$compIdent == "MetFrag")
{
addCall("compounds", "addFormulaScoring", list(
list(value = "compounds"),
list(value = "formulas"),
list(name = "updateScore", value = TRUE)
))
}
}
if (doSusps && input$annotateSus && (nzchar(input$formulaGen) || nzchar(input$compIdent)))
{
addNL()
addComment("Annotate suspects")
addCall("fGroups", "annotateSuspects", list(
list(value = "fGroups"),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", isNULL = !nzchar(input$compIdent)),
list(name = "MSPeakLists", value = "mslists", condition = doMSPL),
list(name = "IDFile", value = "idlevelrules.yml", quote = TRUE, condition = input$genIDLevelFile)
))
}
}
if (input$doTPs)
{
addHeader("Parent and TP linkage")
addComment("You probably want to prioritize the data before componentization. Please see the handbook for more info.")
addCall("componentsTP", "generateComponents", list(
list(value = "fGroups"),
list(value = "tp", quote = TRUE),
list(name = "fGroupsTPs", value = "fGroups"),
list(name = "TPs", value = "TPs"),
list(name = "MSPeakLists", value = "mslists", condition = doMSPL),
list(name = "formulas", value = "formulas", condition = nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", condition = nzchar(input$compIdent))
))
addNL()
addComment("You may want to configure the filtering step below. See the manuals for more details.")
addCall("componentsTP", "filter", list(
list(value = "componentsTP"),
list(name = "retDirMatch", value = FALSE),
list(name = "minSpecSim", value = "NULL"),
list(name = "minSpecSimPrec", value = "NULL"),
list(name = "minSpecSimBoth", value = "NULL"),
list(name = "minFragMatches", value = "NULL"),
list(name = "minNLMatches", value = "NULL"),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen),
condition = input$TPGen == "Logic")
))
addNL()
addComment("Only keep linked feature groups")
addAssignment("fGroups", "fGroups[results = componentsTP]")
}
if (length(input$reportGen) > 0)
{
# UNDONE: for now TP components are always reported instead of others
componVal <- if (input$doTPs)
"componentsTP"
else if (nzchar(input$components) && (!input$selectIons || input$components == "nontarget"))
"components"
else
"NULL"
addHeader("reporting")
if ("HTML" %in% input$reportGen)
{
addComment("Advanced report settings can be edited in the report.yml file.")
addCall(NULL, "report", list(
list(value = "fGroups"),
list(name = "MSPeakLists", value = "mslists", isNULL = !doMSPL),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", isNULL = !nzchar(input$compIdent)),
list(name = "components", value = componVal),
list(name = "TPs", value = "TPs", condition = input$doTPs),
list(name = "settingsFile", value = "report.yml", quote = TRUE),
list(name = "openReport", value = TRUE)
))
}
if ("legacy" %in% input$reportGen)
{
if ("HTML" %in% input$reportGen)
addNL()
addComment("Generate reports with legacy interface.")
addCall(NULL, "reportCSV", condition = "CSV" %in% input$reportLegacy, list(
list(value = "fGroups"),
list(name = "path", value = "report", quote = TRUE),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", isNULL = !nzchar(input$compIdent)),
list(name = "components", value = componVal)
))
addCall(NULL, "reportPDF", condition = "PDF" %in% input$reportLegacy, list(
list(value = "fGroups"),
list(name = "path", value = "report", quote = TRUE),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", isNULL = !nzchar(input$compIdent)),
list(name = "MSPeakLists", value = "mslists", condition = doMSPL),
list(name = "components", value = componVal)
))
addCall(NULL, "reportHTML", condition = "HTML" %in% input$reportLegacy, list(
list(value = "fGroups"),
list(name = "path", value = "report", quote = TRUE),
list(name = "formulas", value = "formulas", isNULL = !nzchar(input$formulaGen)),
list(name = "compounds", value = "compounds", isNULL = !nzchar(input$compIdent)),
list(name = "MSPeakLists", value = "mslists", condition = doMSPL),
list(name = "components", value = componVal),
list(name = "TPs", value = "TPs", condition = input$doTPs),
list(name = "reportPlots", value = c("chord", "venn", "upset", "eics", "formulas"), quote = TRUE),
list(name = "selfContained", value = FALSE),
list(name = "openReport", value = TRUE)
))
}
}
addNL()
return(paste0(textConnectionValue(txtCon), collapse = "\n"))
}
doCreateProject <- function(input, analyses)
{
mkdirp(input$destinationPath)
prepareAnas <- function(anas, tableFile)
{
anas <- copy(anas)
anas[, group := ifelse(!nzchar(group), analysis, group)]
# Make analysis table
if (input$generateAnaInfo == "table")
write.csv(anas[!anas$exclude, c("path", "analysis", "group", "blank", "conc", "norm_conc")],
file.path(input$destinationPath, tableFile), row.names = FALSE)
return(anas)
}
if (input$ionization != "both")
analyses <- prepareAnas(analyses, input$analysisTableFile)
else
analyses <- Map(prepareAnas, analyses, list(input$analysisTableFilePos, input$analysisTableFileNeg))
doSusps <- input$exSuspList || (input$ionization != "both" && nzchar(input$suspectList)) ||
(input$ionization == "both" && nzchar(input$suspectListPos))
if (doSusps && input$annotateSus && input$genIDLevelFile)
genIDLevelRulesFile(file.path(input$destinationPath, "idlevelrules.yml"))
if ("HTML" %in% input$reportGen)
genReportSettingsFile(file.path(input$destinationPath, "report.yml"))
code <- getScriptCode(input, analyses)
if (input$outputScriptTo == "curFile")
{
# insert at end of current document
rstudioapi::insertText(Inf, code, rstudioapi::getSourceEditorContext()$id)
}
else
{
sp <- file.path(input$destinationPath, input$scriptFile)
cat(code, file = sp, sep = "")
if (input$createRStudioProj)
{
rstudioapi::initializeProject(input$destinationPath)
rstudioapi::openProject(input$destinationPath)
}
else
rstudioapi::navigateToFile(sp)
}
}
getTPGenInputs <- function(isLib)
{
ret <- c("Suspect list" = "suspects",
"Screening results" = "screening")
if (isLib)
ret <- c(ret, "All library parents" = "all")
return(ret)
}
getNewProjectUI <- function(destPath)
{
textNote <- function(txt) div(style = "margin: 8px 0 12px; font-size: small", txt)
fileSelect <- function(idText, idButton, label, value = "", ...)
{
fillRow(
flex = c(1, NA),
textInput(idText, label, value, width = "100%", ...),
actionButton(idButton, "", icon("folder-open"), style = "margin: 25px 0 0 15px")
)
}
rangeNumeric <- function(id, label, minVal = 0, maxVal = 0, ...)
{
fillRow(
numericInput(paste0(id, "-min"), paste("Min.", label), value = minVal, ..., width = "95%"),
numericInput(paste0(id, "-max"), paste("Max.", label), value = maxVal, ..., width = "100%")
)
}
miniUI::miniPage(
shinyjs::useShinyjs(),
miniUI::gadgetTitleBar("Create project tool", right = miniUI::miniTitleBarButton("create", "Create", TRUE)),
miniUI::miniTabstripPanel(
miniUI::miniTabPanel(
"General", icon = icon("save"),
miniUI::miniContentPanel(
fillCol(
flex = NA,
fileSelect("destinationPath", "projectDestButton", "Project destination",
if (is.null(destPath)) "~/" else destPath),
br(),
fillRow(
height = 100,
radioButtons("outputScriptTo", "Insert code into", c("New file" = "newFile",
"Current file" = "curFile")),
conditionalPanel(
condition = "input.outputScriptTo == \"newFile\"",
textInput("scriptFile", "Script file", "process.R", width = "80%"),
checkboxInput("createRStudioProj", "Create (and open) RStudio project", value = TRUE)
)
),
br(),
fillRow(
height = 100,
radioButtons("ionization", "Ionization", c("positive", "negative", "both (sets)" = "both"))
)
)
),
miniUI::miniButtonBlock(
actionButton("loadParams", "Load parameters"),
actionButton("saveParams", "Save parameters")
)
),
miniUI::miniTabPanel(
"Analyses", icon = icon("folder-open"),
miniUI::miniContentPanel(
fillCol(
flex = c(NA, NA, 1, NA),
fillRow(
height = 120,
radioButtons("generateAnaInfo", "Generate analysis information",
c("None" = "none", "From new csv file" = "table",
"Load in script" = "script", "Example data" = "example")),
conditionalPanel(
condition = "input.generateAnaInfo == \"table\" || input.generateAnaInfo == \"script\"",
fillCol(
flex = NA,
conditionalPanel(
condition = "input.ionization == \"both\"",
radioButtons("currentSet", "Selected set", c("positive", "negative"),
inline = TRUE)
),
conditionalPanel(
condition = "input.ionization != \"both\" && input.generateAnaInfo == \"table\"",
textInput("analysisTableFile", "Analysis table output file", "analyses.csv")
),
conditionalPanel(
condition = "input.ionization == \"both\" && input.generateAnaInfo == \"table\" && input.currentSet == \"positive\"",
textInput("analysisTableFilePos",
"Analysis table output file", "analyses-pos.csv")
),
conditionalPanel(
condition = "input.ionization == \"both\" && input.generateAnaInfo == \"table\" && input.currentSet == \"negative\"",
textInput("analysisTableFileNeg",
"Analysis table output file", "analyses-neg.csv")
)
)
)
),
conditionalPanel(
condition = "input.generateAnaInfo == \"table\" || input.generateAnaInfo == \"script\"",
fillRow(
height = 30,
textNote("Make sure to consider data conversion if data files are not yet in mzXML/mzML format.")
)
),
conditionalPanel(
condition = "input.generateAnaInfo == \"example\"",
fillRow(
height = 30,
textNote("Make sure that the patRoonData package is installed.")
)
),
conditionalPanel(
condition = "input.generateAnaInfo == \"table\" || input.generateAnaInfo == \"script\"",
flex = NA,
conditionalPanel(
condition = "input.ionization != \"both\"",
rhandsontable::rHandsontableOutput("analysesHot")
),
conditionalPanel(
condition = "input.ionization == \"both\" && input.currentSet == \"positive\"",
rhandsontable::rHandsontableOutput("analysesHotPos")
),
conditionalPanel(
condition = "input.ionization == \"both\" && input.currentSet == \"negative\"",
rhandsontable::rHandsontableOutput("analysesHotNeg")
)
)
)
),
conditionalPanel(
condition = "input.generateAnaInfo == \"table\" || input.generateAnaInfo == \"script\"",
miniUI::miniButtonBlock(
actionButton("addAnalysesDir", "Add analyses from directory ..."),
actionButton("addAnalysesCSV", "Add analyses from csv file ...")
)
)
),
miniUI::miniTabPanel(
"Data pre-treatment", icon = icon("upload"),
miniUI::miniContentPanel(
fillCol(
flex = NA,
height = 220,
fillRow(
height = 75,
selectInput("convAlgo", "Data Conversion Algorithm", c("None" = "", "ProteoWizard" = "pwiz",
"Bruker DataAnalysis" = "bruker",
"OpenMS" = "openms"),
width = "100%")
),
conditionalPanel(
"input.convAlgo != \"\"",
fillRow(
height = 90,
selectInput("convFrom", "Input format", MSFileFormats(), multiple = FALSE,
width = "95%"),
fillCol(
flex = c(1, NA),
selectInput("convTo", "Output format", "mzML", multiple = FALSE,
selected = "mzML", width = "100%"),
textNote("enviPick/XCMS support mzXML, XCMS/OpenMS support mzML")
)
)
),
conditionalPanel(
"input.convAlgo == \"pwiz\" || input.convAlgo == \"bruker\"",
fillRow(
height = 60,
checkboxInput("peakPicking", "Perform peak picking (line spectra)", value = TRUE),
conditionalPanel(
condition = "input.convAlgo == \"pwiz\"",
checkboxInput("peakPickingVendor", "Use vendor algorithm for peak picking", value = TRUE)
)
)
)
),
hr(),
fillCol(
flex = NA,
height = 70,
strong("Bruker DataAnalysis options"),
textNote("Only supported with bruker data and if DataAnalysis is installed.")
),
fillCol(
flex = NA,
height = 120,
fillCol(
flex = NA,
height = 50,
conditionalPanel(
condition = "input.ionization != \"both\"",
fileSelect("DAMethod", "DAMethodButton", "DataAnalysis method"),
),
conditionalPanel(
condition = "input.ionization == \"both\"",
fillRow(
fillCol(
width = "95%",
fileSelect("DAMethodPos", "DAMethodButtonPos", "DataAnalysis method (positive)")
),
fillCol(
width = "95%",
fileSelect("DAMethodNeg", "DAMethodButtonNeg", "DataAnalysis method (negative)")
)
)
)
),
textNote("Leaving this blank will not set any method"),
checkboxInput("doDACalib", "Perform m/z re-calibration")
)
)
),
miniUI::miniTabPanel(
"Features", icon = icon("chart-area"),
miniUI::miniContentPanel(
fillCol(
flex = NA,
fillCol(
height = 90,
flex = NA,
fillRow(
selectInput("featFinder", "Feature finder", c("OpenMS", "XCMS", "enviPick", "SIRIUS", "KPIC2",
"Bruker DataAnalysis" = "Bruker"),
"OpenMS", FALSE, width = "95%"),
fillCol(
flex = c(1, NA),
height = 90,
selectInput("featGrouper", "Feature grouper", c("OpenMS", "XCMS", "KPIC2", "SIRIUS"),
"OpenMS", FALSE, width = "100%"),
conditionalPanel(
condition = "input.featGrouper == \"SIRIUS\"",
textNote(HTML("This will always find <b>and</b> group features with SIRIUS."))
)
)
)
),
fillCol(
height = 125,
flex = NA,
conditionalPanel(
condition = "input.ionization != \"both\"",
fileSelect("suspectList", "suspectListButton", "Suspect list", placeholder = "Leave empty for no suspect screening")
),
conditionalPanel(
condition = "input.ionization == \"both\"",
fillRow(
height = 60,
fillCol(
width = "95%",
fileSelect("suspectListPos", "suspectListButtonPos", "Suspect list (positive)",
placeholder = "Leave empty for no suspect screening")