diff --git a/R/shinyUI.R b/R/shinyUI.R
index f628ae024a767855ae1b59887aaa4f9dd5a5c91f..2f0ab89b02b13362623d6105a7eea06c2e56bac2 100644
--- a/R/shinyUI.R
+++ b/R/shinyUI.R
@@ -679,466 +679,468 @@ shinyScreenApp <- function(projDir=getwd()) {
}})
- shiny::observeEvent(input$mzMLtabSubmB,{
- mzML<-rhandsontable::hot_to_r(input$mzMLtabCtrl)
- rvConf$mzMLtab<-mzML
-
- ## Fill out mz in sets
- sets<-getSets()
- setMode<-mzML$mode[match(sets,mzML$set)]
- names(setMode)<-sets
- nR<-nrow(rvSetId$df)
- dfSet<-rvSetId$df
- dfSet$mz<-rep(NA,nR)
- dfSet$SMILES<-rep(NA,nR)
- dfSet$Name<-rep(NA,nR)
- cmpL<-getCmpL()
- for (s in sets) {
- md<-setMode[[s]]
- ind<-which(dfSet$set==s)
- for (i in ind) {
- id<-dfSet[i,"ID"]
- dfSet[i,"mz"]<-getMzFromCmpL(id,md,cmpL)
- dfSet[i,"SMILES"]<-getSMILESFromCmpL(id,cmpL)
- dfSet[i,"Name"]<-getColFromCmpL(id,"Name",cmpL)
- }
- }
- ## rvSetId$df<-dfSet
- fn<-rvConf$fnLocSetId
- write.csv(file=fn,
- row.names=F,
- x=dfSet)
- message("New set id table written to: ",fn)
- rvConf$impSetIdFn<-fn
- })
-
- shiny::observeEvent(input$impGenRMBB,{
- fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impGenRMBB)
- fn<-fnobj[["datapath"]]
- if (length(fn)>0 && !is.na(fn)) {
- shiny::updateTextInput(session=session,
- inputId="impGenRMBInp",
- value=fn)
- }})
+ ## shiny::observeEvent(input$mzMLtabSubmB,{
+ ## mzML<-rhandsontable::hot_to_r(input$mzMLtabCtrl)
+ ## rvConf$mzMLtab<-mzML
+
+ ## ## Fill out mz in sets
+ ## sets<-getSets()
+ ## nR<-nrow(rvSetId$df)
+ ## dfSet<-rvSetId$df
+ ## dfSet$mz<-rep(NA,nR)
+ ## dfSet$SMILES<-rep(NA,nR)
+ ## dfSet$Name<-rep(NA,nR)
+ ## cmpL<-getCmpL()
+ ## for (s in sets) {
+ ## setMode<-getSetMode(s,mzML)
+
+ ## for md in setMode {
+ ## md<-setMode[[s]]
+ ## ind<-which(dfSet$set==s)
+ ## for (i in ind) {
+ ## id<-dfSet[i,"ID"]
+ ## dfSet[i,"mz"]<-getMzFromCmpL(id,md,cmpL)
+ ## dfSet[i,"SMILES"]<-getSMILESFromCmpL(id,cmpL)
+ ## dfSet[i,"Name"]<-getColFromCmpL(id,"Name",cmpL)
+ ## }
+ ## } #TODO
+ ## }
+ ## ## rvSetId$df<-dfSet
+ ## fn<-rvConf$fnLocSetId
+ ## write.csv(file=fn,
+ ## row.names=F,
+ ## x=dfSet)
+ ## message("New set id table written to: ",fn)
+ ## rvConf$impSetIdFn<-fn
+ ## })
- shiny::observeEvent(input$impCmpListInp,
- {
- impCmpFn<-input$impCmpListInp
- if (length(impCmpFn)>0 && !is.na(impCmpFn) && nchar(impCmpFn)>0) {
- rvConf$impCmpListFn<-impCmpFn
- message("rvConf$impCmpListFn is changed to:",impCmpFn)
+ ## shiny::observeEvent(input$impGenRMBB,{
+ ## fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impGenRMBB)
+ ## fn<-fnobj[["datapath"]]
+ ## if (length(fn)>0 && !is.na(fn)) {
+ ## shiny::updateTextInput(session=session,
+ ## inputId="impGenRMBInp",
+ ## value=fn)
+ ## }})
+
+ ## shiny::observeEvent(input$impCmpListInp,
+ ## {
+ ## impCmpFn<-input$impCmpListInp
+ ## if (length(impCmpFn)>0 && !is.na(impCmpFn) && nchar(impCmpFn)>0) {
+ ## rvConf$impCmpListFn<-impCmpFn
+ ## message("rvConf$impCmpListFn is changed to:",impCmpFn)
- }
- })
+ ## }
+ ## })
- shiny::observeEvent(rvConf$impCmpListFn,
- {
- fn<-rvConf$impCmpListFn
- if (file.exists(fn)) {
- message("Importing compound list from:",fn)
- df<-importCmpList(fn)
- rvCmpList$df<-df
- message("Done importing compound list from: ",fn)
+ ## shiny::observeEvent(rvConf$impCmpListFn,
+ ## {
+ ## fn<-rvConf$impCmpListFn
+ ## if (file.exists(fn)) {
+ ## message("Importing compound list from:",fn)
+ ## df<-importCmpList(fn)
+ ## rvCmpList$df<-df
+ ## message("Done importing compound list from: ",fn)
- }
- })
+ ## }
+ ## })
- shiny::observeEvent(input$impSetIdInp,
- {
- fn<-input$impSetIdInp
- if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
- rvConf$impSetIdFn<-fn
- message("rvConf$impSetIdFn is changed to:",fn)
- }
- })
-
- shiny::observeEvent(input$genFileTabB,{
- fn<-input$confFileTabBase
- if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
- message("Generating basic file table in file ",fn)
- files<-adornmzMLTab(rvConf$mzMLtab,projDir=rvConf$projDir)
- setId<-rvSetId$df
- cmpL<-rvCmpList$df
- df<-genSuprFileTbl(files,setId,destFn=fn)
- df<-addCmpLColsToFileTbl(df,cmpL)
- write.csv(x=df,file=fn,row.names=F)
- rvConf$fnFTBase<-fn
- message("Done generating basic file table in file ",fn)
- }
+ ## shiny::observeEvent(input$impSetIdInp,
+ ## {
+ ## fn<-input$impSetIdInp
+ ## if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
+ ## rvConf$impSetIdFn<-fn
+ ## message("rvConf$impSetIdFn is changed to:",fn)
+ ## }
+ ## })
- })
+ ## shiny::observeEvent(input$genFileTabB,{
+ ## fn<-input$confFileTabBase
+ ## if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
+ ## message("Generating basic file table in file ",fn)
+ ## files<-adornmzMLTab(rvConf$mzMLtab,projDir=rvConf$projDir)
+ ## setId<-rvSetId$df
+ ## cmpL<-rvCmpList$df
+ ## df<-genSuprFileTbl(files,setId,destFn=fn)
+ ## df<-addCmpLColsToFileTbl(df,cmpL)
+ ## write.csv(x=df,file=fn,row.names=F)
+ ## rvConf$fnFTBase<-fn
+ ## message("Done generating basic file table in file ",fn)
+ ## }
- shiny::observeEvent(input$genRunB,{
- FnRMB<-input$impGenRMBInp
- nProc<-as.integer(input$genNoProc)
- fnTab<-rvConf$fnFTBase
- sets<-input$genSetSelInp
- message("Selected sets:")
- message(str(sets))
- message("Number of processes:",nProc)
- message("RMassBank settings file:",FnRMB)
- message("File table:",fnTab)
- if (length(fnTab)>0) {
-
- for (s in sets) {
- message("***** BEGIN set ",s, " *****")
- fnCmpdList<-input$impCmpListInp
- fnStgs<-input$impGenRMBInp
- intTresh<-as.numeric(input$intTresh)
- noiseFac<-as.numeric(input$noiseFac)
- rtDelta<-as.numeric(input$rtDelta)
- ppmLimFine<-as.numeric(input$ppmLimFine)
- dest<-rvConf$projDir
- eicLim<-as.numeric(input$eicLim)
- gc()
- gen(fnFileTab=fnTab,
- fnCmpdList=fnCmpdList,
- fnStgs=fnStgs,
- dest=dest,
- proc=nProc,
- intTresh=intTresh,
- noiseFac=noiseFac,
- rtDelta=rtDelta,
- ppmLimFine=ppmLimFine,
- eicLim=eicLim)
- message("***** END set ",s, " *****")
- }
- gc()
- }})
+ ## })
- shiny::observeEvent(input$genRunPPB,{
- message("Starting preprocessing.")
+ ## shiny::observeEvent(input$genRunB,{
+ ## FnRMB<-input$impGenRMBInp
+ ## nProc<-as.integer(input$genNoProc)
+ ## fnTab<-rvConf$fnFTBase
+ ## sets<-input$genSetSelInp
+ ## message("Selected sets:")
+ ## message(str(sets))
+ ## message("Number of processes:",nProc)
+ ## message("RMassBank settings file:",FnRMB)
+ ## message("File table:",fnTab)
+ ## if (length(fnTab)>0) {
+
+ ## for (s in sets) {
+ ## message("***** BEGIN set ",s, " *****")
+ ## fnCmpdList<-input$impCmpListInp
+ ## fnStgs<-input$impGenRMBInp
+ ## intTresh<-as.numeric(input$intTresh)
+ ## noiseFac<-as.numeric(input$noiseFac)
+ ## rtDelta<-as.numeric(input$rtDelta)
+ ## ppmLimFine<-as.numeric(input$ppmLimFine)
+ ## dest<-rvConf$projDir
+ ## eicLim<-as.numeric(input$eicLim)
+ ## gc()
+ ## gen(fnFileTab=fnTab,
+ ## fnCmpdList=fnCmpdList,
+ ## fnStgs=fnStgs,
+ ## dest=dest,
+ ## proc=nProc,
+ ## intTresh=intTresh,
+ ## noiseFac=noiseFac,
+ ## rtDelta=rtDelta,
+ ## ppmLimFine=ppmLimFine,
+ ## eicLim=eicLim)
+ ## message("***** END set ",s, " *****")
+ ## }
+ ## gc()
+ ## }})
+
+ ## shiny::observeEvent(input$genRunPPB,{
+ ## message("Starting preprocessing.")
- shiny::isolate({
- sets<-getSets()
- cdf<-if (!is.null(rvCmpList$df)) rvCmpList$df else NULL})
+ ## shiny::isolate({
+ ## sets<-getSets()
+ ## cdf<-if (!is.null(rvCmpList$df)) rvCmpList$df else NULL})
- nr<-nrow(cdf)
- if (!is.null(nr)) {
- if (is.na(nr)) nr<-0
- } else nr<-0
- if (length(sets)>0 && nr>0) {
- doneSets<-sets[sapply(sets,isGenDone)]
- if (length(doneSets)>0) {
- fnFullTab<-input$confFileTabProcInp
- fnBaseTab<-input$confFileTabBase
- fnOpen<-""
- fnOpen<-if (file.exists(fnFullTab)) fnFullTab else fnBaseTab
- fullFTab<-read.csv(file=fnOpen,
- comment.char = '',
- stringsAsFactors = F)
-
- doneFTab<-fullFTab[fullFTab$set %in% doneSets,]
- if (nrow(doneFTab)>0) {
- fnTmp<-ppInpFt()
- write.csv(file=fnTmp,
- x=doneFTab,
- row.names=F)
- message("fnTmp: ",fnTmp)
- cmpdL<-rvCmpList$df
- maxId<-do.call(max,as.list(sapply(doneSets,idsFromFiles)))
- intTresh<-as.numeric(input$intTresh)
- noiseFac<-as.numeric(input$noiseFac)
- rtDelta<-as.numeric(input$rtDelta)
- ## dr<-file.path(dirname(fnCand),sets)
- preProc(fnFileTab=fnTmp,
- lCmpdList=maxId,
- fnDest=fnTmp,
- intTresh=intTresh,
- noiseFac=noiseFac,
- rtDelta=rtDelta)
- ppFnTab<-read.csv(file=fnTmp,
- comment.char = '',
- stringsAsFactors = F)
- extNms<-names(ppFnTab)
- basNms<-names(fullFTab)
- diffNms<-setdiff(extNms,basNms)
- nrf<-nrow(fullFTab)
- for (nm in diffNms) {
- z<-logical(length=nrf)
- z<-T
- fullFTab[[nm]]<-z
- }
- fullFTab[fullFTab$set %in% doneSets,]<-ppFnTab
- write.csv(file=fnFullTab,
- x=fullFTab,
- row.names=F)
- file.copy(fnFullTab,input$confResFileTab,overwrite=T)
- message("Finished preprocessing.")
+ ## nr<-nrow(cdf)
+ ## if (!is.null(nr)) {
+ ## if (is.na(nr)) nr<-0
+ ## } else nr<-0
+ ## if (length(sets)>0 && nr>0) {
+ ## doneSets<-sets[sapply(sets,isGenDone)]
+ ## if (length(doneSets)>0) {
+ ## fnFullTab<-input$confFileTabProcInp
+ ## fnBaseTab<-input$confFileTabBase
+ ## fnOpen<-""
+ ## fnOpen<-if (file.exists(fnFullTab)) fnFullTab else fnBaseTab
+ ## fullFTab<-read.csv(file=fnOpen,
+ ## comment.char = '',
+ ## stringsAsFactors = F)
+
+ ## doneFTab<-fullFTab[fullFTab$set %in% doneSets,]
+ ## if (nrow(doneFTab)>0) {
+ ## fnTmp<-ppInpFt()
+ ## write.csv(file=fnTmp,
+ ## x=doneFTab,
+ ## row.names=F)
+ ## message("fnTmp: ",fnTmp)
+ ## cmpdL<-rvCmpList$df
+ ## maxId<-do.call(max,as.list(sapply(doneSets,idsFromFiles)))
+ ## intTresh<-as.numeric(input$intTresh)
+ ## noiseFac<-as.numeric(input$noiseFac)
+ ## rtDelta<-as.numeric(input$rtDelta)
+ ## ## dr<-file.path(dirname(fnCand),sets)
+ ## preProc(fnFileTab=fnTmp,
+ ## lCmpdList=maxId,
+ ## fnDest=fnTmp,
+ ## intTresh=intTresh,
+ ## noiseFac=noiseFac,
+ ## rtDelta=rtDelta)
+ ## ppFnTab<-read.csv(file=fnTmp,
+ ## comment.char = '',
+ ## stringsAsFactors = F)
+ ## extNms<-names(ppFnTab)
+ ## basNms<-names(fullFTab)
+ ## diffNms<-setdiff(extNms,basNms)
+ ## nrf<-nrow(fullFTab)
+ ## for (nm in diffNms) {
+ ## z<-logical(length=nrf)
+ ## z<-T
+ ## fullFTab[[nm]]<-z
+ ## }
+ ## fullFTab[fullFTab$set %in% doneSets,]<-ppFnTab
+ ## write.csv(file=fnFullTab,
+ ## x=fullFTab,
+ ## row.names=F)
+ ## file.copy(fnFullTab,input$confResFileTab,overwrite=T)
+ ## message("Finished preprocessing.")
- }
- }
- }
- })
+ ## }
+ ## }
+ ## }
+ ## })
- shiny::observeEvent(input$presSelCmpd,{
- pos<-input$presSelCmpd
- rvConf$currIDSel<-as.numeric(pos)
- })
+ ## shiny::observeEvent(input$presSelCmpd,{
+ ## pos<-input$presSelCmpd
+ ## rvConf$currIDSel<-as.numeric(pos)
+ ## })
- shiny::observeEvent(input$presPrev,{
- len<-length(rvConf$currIDSet)
- x<-rvConf$currIDSel-1
- if (x>0) rvConf$currIDSel<-x
- })
+ ## shiny::observeEvent(input$presPrev,{
+ ## len<-length(rvConf$currIDSet)
+ ## x<-rvConf$currIDSel-1
+ ## if (x>0) rvConf$currIDSel<-x
+ ## })
- shiny::observeEvent(input$presNext,{
- len<-length(rvConf$currIDSet)
- x<-rvConf$currIDSel+1
- if (x<=len) rvConf$currIDSel<-x
- })
+ ## shiny::observeEvent(input$presNext,{
+ ## len<-length(rvConf$currIDSet)
+ ## x<-rvConf$currIDSel+1
+ ## if (x<=len) rvConf$currIDSel<-x
+ ## })
- shiny::observeEvent(rvConf$fnFT,{
- fn<-rvConf$fnFT
- if (!is.null(fn) && file.exists(fn)) {
- rvConf$fTab<-read.csv(file=fn,
- comment.char = '',
- stringsAsFactors = F)
- }
- })
+ ## shiny::observeEvent(rvConf$fnFT,{
+ ## fn<-rvConf$fnFT
+ ## if (!is.null(fn) && file.exists(fn)) {
+ ## rvConf$fTab<-read.csv(file=fn,
+ ## comment.char = '',
+ ## stringsAsFactors = F)
+ ## }
+ ## })
- shiny::observeEvent(rvConf$currIDSel,{
- ids<-rvConf$currIDSet
- if (length(ids)>0) rvConf$currID<-ids[[rvConf$currIDSel]]
- })
+ ## shiny::observeEvent(rvConf$currIDSel,{
+ ## ids<-rvConf$currIDSet
+ ## if (length(ids)>0) rvConf$currID<-ids[[rvConf$currIDSel]]
+ ## })
- shiny::observeEvent(input$submitQA,{
- res <- lapply(rvConf$tags,getCheckboxValues,input,rvConf)
- names(res) <- rvConf$tags
- rvConf$fTab <- updateFileTable(df=rvConf$fTab,
- set=input$presSelSet,
- id=rvConf$currID,
- linput=res)
- })
+ ## shiny::observeEvent(input$submitQA,{
+ ## res <- lapply(rvConf$tags,getCheckboxValues,input,rvConf)
+ ## names(res) <- rvConf$tags
+ ## rvConf$fTab <- updateFileTable(df=rvConf$fTab,
+ ## set=input$presSelSet,
+ ## id=rvConf$currID,
+ ## linput=res)
+ ## })
- shiny::observeEvent(input$savefiletable,
- {
- fn<-input$fn_ftable
- message("Writing current file table to ",fn)
- write.csv(file=fn,x=rvConf$fTab,row.names = F)
- })
+ ## shiny::observeEvent(input$savefiletable,
+ ## {
+ ## fn<-input$fn_ftable
+ ## message("Writing current file table to ",fn)
+ ## write.csv(file=fn,x=rvConf$fTab,row.names = F)
+ ## })
- shiny::observeEvent(input$saveplot,
- {
- i=rvConf$currID
- pfn <-input$plotname
- if (is.na(pfn)) pfn <- "plotCpdID_%i.pdf"
- fn <- sprintf(pfn,i)
- rtrange <- c(input$min_val,input$max_val)
- pdf(file=fn, width=12, height=8)
- rvPres$plot_id(i,rtrange=rtrange, log=input$yaxis)
- dev.off()
- message("Plotting compound ", i," to ",fn," done.")
- })
+ ## shiny::observeEvent(input$saveplot,
+ ## {
+ ## i=rvConf$currID
+ ## pfn <-input$plotname
+ ## if (is.na(pfn)) pfn <- "plotCpdID_%i.pdf"
+ ## fn <- sprintf(pfn,i)
+ ## rtrange <- c(input$min_val,input$max_val)
+ ## pdf(file=fn, width=12, height=8)
+ ## rvPres$plot_id(i,rtrange=rtrange, log=input$yaxis)
+ ## dev.off()
+ ## message("Plotting compound ", i," to ",fn," done.")
+ ## })
- shiny::observeEvent(input$saveallplots,
- {
- i=rvConf$currID
- pfn <-input$plotname
- if (is.na(pfn)) pfn <- "plotall.pdf"
- fn <- sprintf(pfn,i)
- pdf(file=fn, width=12, height=8)
- for (i in rvConf$currIDSet) {
- rvPres$plot_id(i,log=input$yaxis)
- message("Plotting compound ", i," done.")
- }
- dev.off()
- })
- ## ***** Observe *****
- shiny::observe({
- fchoice<-shinyFiles::parseFilePaths(root=volumes,input$mzMLB)
- paths<-fchoice[["datapath"]]
- isolate({
- for (pt in paths) {
- rvConf$mzMLtab<-extd_mzMLtab(rvConf$mzMLtab,pt)
- }
+ ## shiny::observeEvent(input$saveallplots,
+ ## {
+ ## i=rvConf$currID
+ ## pfn <-input$plotname
+ ## if (is.na(pfn)) pfn <- "plotall.pdf"
+ ## fn <- sprintf(pfn,i)
+ ## pdf(file=fn, width=12, height=8)
+ ## for (i in rvConf$currIDSet) {
+ ## rvPres$plot_id(i,log=input$yaxis)
+ ## message("Plotting compound ", i," done.")
+ ## }
+ ## dev.off()
+ ## })
+ ## ## ***** Observe *****
+ ## shiny::observe({
+ ## fchoice<-shinyFiles::parseFilePaths(root=volumes,input$mzMLB)
+ ## paths<-fchoice[["datapath"]]
+ ## isolate({
+ ## for (pt in paths) {
+ ## rvConf$mzMLtab<-extd_mzMLtab(rvConf$mzMLtab,pt)
+ ## }
- })
- })
+ ## })
+ ## })
- shiny::observe({
- rvConf$currIDSel
- shiny::updateSelectInput(session=session,
- inputId="presSelCmpd",
- selected=rvConf$currIDSel)
- })
- shiny::observe({
- shiny::invalidateLater(100,
- session=session)
- output$genTabProcCtrl<-rhandsontable::renderRHandsontable({
- sets<-getSets()
- genState<-sapply(sets,isGenDone)
- df<-if (!is.null(sets)) {data.frame(set=sets,
- generated=genState,
- stringsAsFactors=F)
- } else {data.frame(sets=character(),
- generated=logical(),
- stringsAsFactors=F)}
- rhandsontable::rhandsontable(df,
- rowHeaders=NULL,
- readOnly=T,
- stretchH="all")
+ ## shiny::observe({
+ ## rvConf$currIDSel
+ ## shiny::updateSelectInput(session=session,
+ ## inputId="presSelCmpd",
+ ## selected=rvConf$currIDSel)
+ ## })
+ ## shiny::observe({
+ ## shiny::invalidateLater(100,
+ ## session=session)
+ ## output$genTabProcCtrl<-rhandsontable::renderRHandsontable({
+ ## sets<-getSets()
+ ## genState<-sapply(sets,isGenDone)
+ ## df<-if (!is.null(sets)) {data.frame(set=sets,
+ ## generated=genState,
+ ## stringsAsFactors=F)
+ ## } else {data.frame(sets=character(),
+ ## generated=logical(),
+ ## stringsAsFactors=F)}
+ ## rhandsontable::rhandsontable(df,
+ ## rowHeaders=NULL,
+ ## readOnly=T,
+ ## stretchH="all")
- })
- })
+ ## })
+ ## })
- shiny::observe({
- shiny::invalidateLater(100,
- session=session)
- fnFT<-if (file.exists(input$confResFileTab)) input$confResFileTab else NULL
- rvConf$fnFT<-fnFT
+ ## shiny::observe({
+ ## shiny::invalidateLater(100,
+ ## session=session)
+ ## fnFT<-if (file.exists(input$confResFileTab)) input$confResFileTab else NULL
+ ## rvConf$fnFT<-fnFT
- })
+ ## })
- shiny::observe({
- sets<-getSets()
- if (length(sets)>0 && !is.na(sets)) {
- message("Bef upd inputs")
- shiny::updateSelectInput(session=session,
- "presSelSet",
- choices=sets,
- selected=sets[[1]])
- message("upd sel worked")
- }
- })
+ ## shiny::observe({
+ ## sets<-getSets()
+ ## if (length(sets)>0 && !is.na(sets)) {
+ ## message("Bef upd inputs")
+ ## shiny::updateSelectInput(session=session,
+ ## "presSelSet",
+ ## choices=sets,
+ ## selected=sets[[1]])
+ ## message("upd sel worked")
+ ## }
+ ## })
- shiny::observe({
- i<-rvConf$currID
- spectProps<-rvConf$spectProps
- set<-input$presSelSet
- if (!is.na(i) && length(spectProps)>0) {
- message("Updating QA checkboxes.")
- QANAMES<-rvConf$QANAMES
- sdf <- queryFileTable(df=rvConf$fTab,set=set,id=i)
- sdf$tag<-as.character(sdf$tag)
- for (t in sdf$tag) {
- sprop <- rvConf$spectProps[[t]]
- sdfSel<-sdf[sdf$tag %in% t,QANAMES]
- sel <- as.logical(sdfSel)
- choices <- QANAMES[sel]
- names(choices) <- QANAMES[sel]
- shiny::updateCheckboxGroupInput(session = session,inputId = sprop,selected=choices)
- }
- message("Updating QA checkboxes done.")
+ ## shiny::observe({
+ ## i<-rvConf$currID
+ ## spectProps<-rvConf$spectProps
+ ## set<-input$presSelSet
+ ## if (!is.na(i) && length(spectProps)>0) {
+ ## message("Updating QA checkboxes.")
+ ## QANAMES<-rvConf$QANAMES
+ ## sdf <- queryFileTable(df=rvConf$fTab,set=set,id=i)
+ ## sdf$tag<-as.character(sdf$tag)
+ ## for (t in sdf$tag) {
+ ## sprop <- rvConf$spectProps[[t]]
+ ## sdfSel<-sdf[sdf$tag %in% t,QANAMES]
+ ## sel <- as.logical(sdfSel)
+ ## choices <- QANAMES[sel]
+ ## names(choices) <- QANAMES[sel]
+ ## shiny::updateCheckboxGroupInput(session = session,inputId = sprop,selected=choices)
+ ## }
+ ## message("Updating QA checkboxes done.")
+
+ ## }
+ ## })
- }
- })
+ ## shiny::observe({
+ ## sets<-getSets()
+ ## set<-input$presSelSet
+ ## if (!nchar(set)==0) {
+ ## cmpdL<-getCmpL()
+ ## setID<-getSetId()
+ ## rvConf$currSet<-set
+ ## }
+ ## })
- shiny::observe({
- sets<-getSets()
- set<-input$presSelSet
- if (!nchar(set)==0) {
- cmpdL<-getCmpL()
- setID<-getSetId()
- rvConf$currSet<-set
- }
- })
+ ## shiny::observe({
+ ## message("currSet START")
+ ## currSetMkCmpMenu()
+ ## currSetPreCalc()
+ ## message("currSet END")
- shiny::observe({
- message("currSet START")
- currSetMkCmpMenu()
- currSetPreCalc()
- message("currSet END")
+ ## })
- })
+ ## shiny::observe({
+ ## input$restoreConfB
+ ## message("Restore event observed.")
+ ## restoreConf()
+ ## message("Restore event finished.")
+ ## })
- shiny::observe({
- input$restoreConfB
- message("Restore event observed.")
- restoreConf()
- message("Restore event finished.")
- })
+ ## ## shiny::observe({
+ ## ## rvConf$tags<-getTags()
+ ## ## })
## shiny::observe({
- ## rvConf$tags<-getTags()
+ ## message("Update tags and sets.")
+ ## update_sets_mzMLtab()
+ ## update_tags_mzMLtab()
+ ## message("Done updating tags and sets.")
## })
- shiny::observe({
- message("Update tags and sets.")
- update_sets_mzMLtab()
- update_tags_mzMLtab()
- message("Done updating tags and sets.")
- })
-
- shiny::observe(
- {
- fn<-rvConf$impSetIdFn
- if (file.exists(fn)) {
- message("Importing compound sets from:",fn)
- rvSetId$df<-readSetId(fn)
- message("Done importing compound sets from: ",fn)
- }
- df<-rvSetId$df
- if (length(df)>0 && !is.na(df) && nrow(df)>0) {
- shiny::updateSelectInput(session=session,
- inputId="genSetSelInp",
- choices=levels(df$set))
- }
- shiny::isolate({
- message("Changing the inpSetIdFn to: ",fn, " in isolation.")
- shiny::updateTextInput(session=session,
- inputId="impSetIdInp",
- value=fn)
- })
- })
+ ## shiny::observe(
+ ## {
+ ## fn<-rvConf$impSetIdFn
+ ## if (file.exists(fn)) {
+ ## message("Importing compound sets from:",fn)
+ ## rvSetId$df<-readSetId(fn)
+ ## message("Done importing compound sets from: ",fn)
+ ## }
+ ## df<-rvSetId$df
+ ## if (length(df)>0 && !is.na(df) && nrow(df)>0) {
+ ## shiny::updateSelectInput(session=session,
+ ## inputId="genSetSelInp",
+ ## choices=levels(df$set))
+ ## }
+ ## shiny::isolate({
+ ## message("Changing the inpSetIdFn to: ",fn, " in isolation.")
+ ## shiny::updateTextInput(session=session,
+ ## inputId="impSetIdInp",
+ ## value=fn)
+ ## })
+ ## })
- ## ***** Render *****
- output$cmpListCtrl <- rhandsontable::renderRHandsontable({
- df<-rvCmpList$df
- rhandsontable::rhandsontable(df,stretchH="all")
- })
+ ## ## ***** Render *****
+ ## output$cmpListCtrl <- rhandsontable::renderRHandsontable({
+ ## df<-rvCmpList$df
+ ## rhandsontable::rhandsontable(df,stretchH="all")
+ ## })
- output$setIdTabCtrl<- rhandsontable::renderRHandsontable({
- df<-rvSetId$df
- rhandsontable::rhandsontable(df,stretchH="all")
- })
+ ## output$setIdTabCtrl<- rhandsontable::renderRHandsontable({
+ ## df<-rvSetId$df
+ ## rhandsontable::rhandsontable(df,stretchH="all")
+ ## })
- output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
- if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all") else NULL
- })
+ ## output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
+ ## if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all") else NULL
+ ## })
- output$nvPanel<-shiny::renderUI({
- message("Rendering panel started")
- ft<-rvConf$fTab
- set<-input$presSelSet
- if (nchar(set)>0 && !is.null(ft)) {
- QANms<-rvConf$QANAMES
- names(QANms)<-QANms
- tags<-levels(factor(ft[ft$set==set,]$tag))
- rvConf$tags<-tags
- spectProps<-sapply(tags,function (tag) paste("spectProps",tag,sep=""))
- rvConf$spectProps<-spectProps
- tabPanelList <- lapply(tags, function(tag) {
- shiny::tabPanel(tag, shiny::checkboxGroupInput(spectProps[[tag]], "Quality Control",
- QANms),
- shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
- shiny::verbatimTextOutput(paste("value",tag,sep=""))
- )})
+ ## output$nvPanel<-shiny::renderUI({
+ ## message("Rendering panel started")
+ ## ft<-rvConf$fTab
+ ## set<-input$presSelSet
+ ## if (nchar(set)>0 && !is.null(ft)) {
+ ## QANms<-rvConf$QANAMES
+ ## names(QANms)<-QANms
+ ## tags<-levels(factor(ft[ft$set==set,]$tag))
+ ## rvConf$tags<-tags
+ ## spectProps<-sapply(tags,function (tag) paste("spectProps",tag,sep=""))
+ ## rvConf$spectProps<-spectProps
+ ## tabPanelList <- lapply(tags, function(tag) {
+ ## shiny::tabPanel(tag, shiny::checkboxGroupInput(spectProps[[tag]], "Quality Control",
+ ## QANms),
+ ## shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
+ ## shiny::verbatimTextOutput(paste("value",tag,sep=""))
+ ## )})
- do.call(shiny::navlistPanel, tabPanelList)
- message("done rendering panel")
- } else NULL
- })
+ ## do.call(shiny::navlistPanel, tabPanelList)
+ ## message("done rendering panel")
+ ## } else NULL
+ ## })
- output$chromGram <- renderPlot(
- {
- plot_id<-rvPres$plot_id
- i=rvConf$currID
- rtrange <- c(input$min_val,input$max_val)
- if (!is.null(plot_id)) {
- plot_id(i,rtrange=rtrange, log=input$yaxis)
- }
- })
+ ## output$chromGram <- renderPlot(
+ ## {
+ ## plot_id<-rvPres$plot_id
+ ## i=rvConf$currID
+ ## rtrange <- c(input$min_val,input$max_val)
+ ## if (!is.null(plot_id)) {
+ ## plot_id(i,rtrange=rtrange, log=input$yaxis)
+ ## }
+ ## })
session$onSessionEnded(function () stopApp())