diff --git a/R/mix.R b/R/mix.R
index f803c556029afadea2c888ade09a84ad3a2d8121..02ac9a32db9f4d41e2f850ed881cf668a18a3bb4 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -21,6 +21,28 @@ RT_DIGITS=2
M_DIGITS=4
PAL="Dark2"
+REST_TXT_INP<-c("impGenRMBInp",
+ "impCmpListInp",
+ "impSetIdInp",
+ "tagsInp",
+ "confFileTabBase",
+ "confFileTabProcInp",
+ "confResFileTab")
+
+## ***** Helper Functions *****
+tab2file<-function(tab,file,...) {
+ write.csv(x=tab,file=file,...)
+}
+
+file2tab<-function(file,stringsAsFactors=F,comment.char='',...) {
+ read.csv(file=file,
+ header=T,
+ stringsAsFactors=stringsAsFactors,
+ comment.char=comment.char,
+ na.strings=c("","NA"))
+}
+
+## ***** End helper functions *****
ppInpFt<-function() {
tempfile(pattern=FN_PP_OUT_PREF,fileext=".csv")
}
diff --git a/R/shinyUI.R b/R/shinyUI.R
index 2f0ab89b02b13362623d6105a7eea06c2e56bac2..0f0184fc6ad2e2489d3e1fb8d63bd80c56ff28c7 100644
--- a/R/shinyUI.R
+++ b/R/shinyUI.R
@@ -106,7 +106,7 @@ mkUI <- function() {
## ***** Compound List Tab *****
cmpListBox<-shinydashboard::box(title="Compound list",
- rhandsontable::rHandsontableOutput("cmpListCtrl"),
+ rhandsontable::rHandsontableOutput("tgtCtrl"),
width=NULL)
cmpListLayout <- shiny::fluidRow(shiny::column(cmpListBox,
@@ -119,7 +119,7 @@ mkUI <- function() {
## ***** Sets of compounds *****
setIdBox<-shinydashboard::box(title="Compound sets",
- rhandsontable::rHandsontableOutput("setIdTabCtrl"),
+ rhandsontable::rHandsontableOutput("setIdCtrl"),
width = NULL)
setIdLayout<-shiny::fluidRow(shiny::column(setIdBox,
@@ -447,12 +447,12 @@ shinyScreenApp <- function(projDir=getwd()) {
server <- function(input,output,session) {
## ***** reactive values *****
- rvConf <- shiny::reactiveValues(mzMLtab=mk_mzMLtab(),
- tags=list(),
+ rvConf <- shiny::reactiveValues(tags=list(),
sets=list(),
spectProps=list(),
QANAMES=QANAMES,
MODEMAP=MODEMAP,
+ REST_TXT_INP=REST_TXT_INP,
impCmpListFn="",
impSetIdFn="",
impGenRMBFn="",
@@ -466,11 +466,13 @@ shinyScreenApp <- function(projDir=getwd()) {
currIDSel=1,
currIDSet=list(),
currID=NA,
- fnFT=NULL,
- fTab=NULL)
-
- rvCmpList<- shiny::reactiveValues(df=mk_cmpList())
- rvSetId<- shiny::reactiveValues(df=mk_setId())
+ fnFT=NULL)
+ rvTab<-shiny::reactiveValues(
+ mzML=NULL, # files (File), sets (set) and mode (mode)
+ tgt=NULL, # ids(ID),SMILES(SMILES) and names (Name)
+ setId=NULL, # ids(ID), sets (set)
+ mzMode=NULL, #ids (ID),masses(mz) and modes(mode)
+ mtr=NULL) #master table (everything combined)
rvPres<-shiny::reactiveValues(cex=CEX,
rt_digits=RT_DIGITS,
m_digits=M_DIGITS,
@@ -494,30 +496,30 @@ shinyScreenApp <- function(projDir=getwd()) {
})
getSets<-shiny::reactive({
- levels(rvSetId$df$set)
+ levels(rvTab$setId$set)
})
getCmpL<-shiny::reactive({
- rvCmpList$df #rhandsontable::hot_to_r(input$cmpListCtrl)
+ rvTab$tgt #rhandsontable::hot_to_r(input$tgtCtrl)
})
getSetId<-shiny::reactive({
- rvSetId$df #rhandsontable::hot_to_r(input$setIdTabCtrl)
+ rvTab$setId #rhandsontable::hot_to_r(input$setIdCtrl)
})
update_tags_mzMLtab<-shiny::reactive({
input$tagsInp
tags<-getTags()
- tagCol<-rvConf$mzMLtab$tag
- if (length(levels(tagCol))==0) rvConf$mzMLtab$tag<-factor(tagCol)
- rvConf$mzMLtab$tag<-factor(tagCol,levels=tags)
+ tagCol<-rvTab$mzML$tag
+ if (length(levels(tagCol))==0) rvTab$mzML$tag<-factor(tagCol)
+ rvTab$mzML$tag<-factor(tagCol,levels=tags)
})
update_sets_mzMLtab<-shiny::reactive({
sets<-getSets()
- setCol<-rvConf$mzMLtab$set
- if (length(levels(setCol))==0) rvConf$mzMLtab$set<-factor(setCol)
- rvConf$mzMLtab$set<-factor(setCol,levels=sets)
+ setCol<-rvTab$mzML$set
+ if (length(levels(setCol))==0) rvTab$mzML$set<-factor(setCol)
+ rvTab$mzML$set<-factor(setCol,levels=sets)
})
saveConf<-reactive({
@@ -535,6 +537,7 @@ shinyScreenApp <- function(projDir=getwd()) {
sav$input$impCmpListInp<-input$impCmpListInp
sav$input$impSetIdInp<-input$impSetIdInp
sav$input$impGenRMBInp<-input$impGenRMBInp
+ sav$tab<-rvTab
saveRDS(object=sav,file=fn)
}
})
@@ -546,41 +549,17 @@ shinyScreenApp <- function(projDir=getwd()) {
if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
message("Restoring config from",fn)
sav<-readRDS(fn)
- ## shiny::isolate({
- ## sav<-readRDS(fn)
- ## for (nm in names(sav$rvConf)) {
- ## rvConf[[nm]]<-sav$rvConf[[nm]]
- ## }
- shiny::updateTextInput(session=session,
- inputId="impGenRMBInp",
- value=sav$input$impGenRMBInp)
- shiny::updateTextInput(session=session,
- inputId="impCmpListInp",
- value=sav$input$impCmpListInp)
- shiny::updateTextInput(session=session,
- inputId="impSetIdInp",
- value=sav$input$impSetIdInp)
- shiny::updateTextInput(session=session,
- inputId="tagsInp",
- value=sav$input$tagsInp)
- shiny::updateTextInput(session=session,
- inputId="confFileTabBase",
- value=sav$input$confFileTabBase)
- shiny::updateTextInput(session=session,
- inputId="confFileTabProcInp",
- value=sav$input$confFileTabProcInp)
- shiny::updateTextInput(session=session,
- inputId="confResFileTab",
- value=sav$input$confResFileTab)
-
- rvConf$mzMLtab<-sav$rvConf$mzMLtab
+ for (nm in rvConf$REST_TXT_INP) {
+ shiny::updateTextInput(session=session,
+ inputId=nm,
+ value=sav$input[[nm]])
+ }
rvConf$fnFTBase<-sav$rvConf$fnFTBase
rvConf$fnFT<-sav$rvConf$fnFT
-
-
-
-
+ for (nm in names(rvTab)) {
+ rvTab[[nm]]<-sav$rvTab[[nm]]
+ }
}
})
@@ -605,7 +584,7 @@ shinyScreenApp <- function(projDir=getwd()) {
})
currSetPreCalc<-shiny::reactive({
set<-rvConf$currSet
- fTab<-rvConf$fTab
+ fTab<-rvTab$mtr
if (!is.na(set) && length(fTab)>0) {
setId<-getSetId()
@@ -620,7 +599,7 @@ shinyScreenApp <- function(projDir=getwd()) {
tags<-levels(factor(sfTab$tag))
iTag<- match(tags,sfTab$tag)
wd<-sfTab$wd[iTag]
- cmpL<-rvCmpList$df
+ cmpL<-rvTab$tgt
preID<-setIdIds
smiles<-setIdSMILES
@@ -658,6 +637,12 @@ shinyScreenApp <- function(projDir=getwd()) {
saveConf()
})
+ shiny::observeEvent(input$restoreConfB,{
+ message("Restore event observed.")
+ restoreConf()
+ message("Restore event finished.")
+ })
+
shiny::observeEvent(input$impSetIdB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impSetIdB)
@@ -681,12 +666,12 @@ shinyScreenApp <- function(projDir=getwd()) {
## shiny::observeEvent(input$mzMLtabSubmB,{
## mzML<-rhandsontable::hot_to_r(input$mzMLtabCtrl)
- ## rvConf$mzMLtab<-mzML
+ ## rvTab$mzML<-mzML
## ## Fill out mz in sets
## sets<-getSets()
- ## nR<-nrow(rvSetId$df)
- ## dfSet<-rvSetId$df
+ ## nR<-nrow(rvTab$setId)
+ ## dfSet<-rvTab$setId
## dfSet$mz<-rep(NA,nR)
## dfSet$SMILES<-rep(NA,nR)
## dfSet$Name<-rep(NA,nR)
@@ -705,7 +690,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## }
## } #TODO
## }
- ## ## rvSetId$df<-dfSet
+ ## ## rvTab$setId<-dfSet
## fn<-rvConf$fnLocSetId
## write.csv(file=fn,
## row.names=F,
@@ -723,45 +708,67 @@ shinyScreenApp <- function(projDir=getwd()) {
## 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(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$impCmpListFn
+ if (file.exists(fn)) {
+ message("Importing compound list from:",fn)
+ df<-file2tab(file=fn)
+ rvTab$tgt<-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$impSetIdInp,
+ {
+ fn<-input$impSetIdInp
+ if (length(fn)>0 && !is.na(fn) && nchar(fn)>0) {
+ rvConf$impSetIdFn<-fn
+ message("rvConf$impSetIdFn is changed to:",fn)
+ }
+ })
+
+ shiny::observeEvent(rvConf$impSetIdFn,
+ {
+ fn<-rvConf$impSetIdFn
+ if (file.exists(fn)) {
+ message("Importing compound sets from:",fn)
+ rvTab$setId<-file2tab(file=fn)
+ message("Done importing compound sets from: ",fn)
+ }
+ ## df<-rvTab$setId
+ ## if (length(df)>0 && !is.na(df) && nrow(df)>0) {
+ ## shiny::updateSelectInput(session=session,
+ ## inputId="genSetSelInp",
+ ## choices=levels(df$set))
+ ## }
+ ## shiny::isolate({
+ ## message("Changing the inpSetIdFn to: ",fn, " in isolation.")
+ ## shiny::updateTextInput(session=session,
+ ## inputId="impSetIdInp",
+ ## value=fn)
+ ## })
+ })
## shiny::observeEvent(input$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$df
+ ## files<-adornmzMLTab(rvTab$mzML,projDir=rvConf$projDir)
+ ## setId<-rvTab$setId
+ ## cmpL<-rvTab$tgt
## df<-genSuprFileTbl(files,setId,destFn=fn)
## df<-addCmpLColsToFileTbl(df,cmpL)
## write.csv(x=df,file=fn,row.names=F)
@@ -814,7 +821,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## shiny::isolate({
## sets<-getSets()
- ## cdf<-if (!is.null(rvCmpList$df)) rvCmpList$df else NULL})
+ ## cdf<-if (!is.null(rvTab$tgt)) rvTab$tgt else NULL})
## nr<-nrow(cdf)
## if (!is.null(nr)) {
@@ -838,7 +845,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## x=doneFTab,
## row.names=F)
## message("fnTmp: ",fnTmp)
- ## cmpdL<-rvCmpList$df
+ ## cmpdL<-rvTab$tgt
## maxId<-do.call(max,as.list(sapply(doneSets,idsFromFiles)))
## intTresh<-as.numeric(input$intTresh)
## noiseFac<-as.numeric(input$noiseFac)
@@ -895,7 +902,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## shiny::observeEvent(rvConf$fnFT,{
## fn<-rvConf$fnFT
## if (!is.null(fn) && file.exists(fn)) {
- ## rvConf$fTab<-read.csv(file=fn,
+ ## rvTab$mtr<-read.csv(file=fn,
## comment.char = '',
## stringsAsFactors = F)
## }
@@ -910,7 +917,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## shiny::observeEvent(input$submitQA,{
## res <- lapply(rvConf$tags,getCheckboxValues,input,rvConf)
## names(res) <- rvConf$tags
- ## rvConf$fTab <- updateFileTable(df=rvConf$fTab,
+ ## rvTab$mtr <- updateFileTable(df=rvTab$mtr,
## set=input$presSelSet,
## id=rvConf$currID,
## linput=res)
@@ -920,7 +927,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## {
## fn<-input$fn_ftable
## message("Writing current file table to ",fn)
- ## write.csv(file=fn,x=rvConf$fTab,row.names = F)
+ ## write.csv(file=fn,x=rvTab$mtr,row.names = F)
## })
@@ -956,7 +963,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## paths<-fchoice[["datapath"]]
## isolate({
## for (pt in paths) {
- ## rvConf$mzMLtab<-extd_mzMLtab(rvConf$mzMLtab,pt)
+ ## rvTab$mzML<-extd_mzMLtab(rvTab$mzML,pt)
## }
## })
@@ -1017,7 +1024,7 @@ shinyScreenApp <- function(projDir=getwd()) {
## if (!is.na(i) && length(spectProps)>0) {
## message("Updating QA checkboxes.")
## QANAMES<-rvConf$QANAMES
- ## sdf <- queryFileTable(df=rvConf$fTab,set=set,id=i)
+ ## sdf <- queryFileTable(df=rvTab$mtr,set=set,id=i)
## sdf$tag<-as.character(sdf$tag)
## for (t in sdf$tag) {
## sprop <- rvConf$spectProps[[t]]
@@ -1050,13 +1057,6 @@ shinyScreenApp <- function(projDir=getwd()) {
## })
- ## shiny::observe({
- ## input$restoreConfB
- ## message("Restore event observed.")
- ## restoreConf()
- ## message("Restore event finished.")
- ## })
-
## ## shiny::observe({
## ## rvConf$tags<-getTags()
## ## })
@@ -1068,50 +1068,25 @@ shinyScreenApp <- function(projDir=getwd()) {
## 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)
- ## })
- ## })
-
+ ## ***** Render *****
+ output$tgtCtrl <- rhandsontable::renderRHandsontable({
+ df<-rvTab$tgt
+ 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$setIdCtrl<- rhandsontable::renderRHandsontable({
+ df<-rvTab$setId
+ rhandsontable::rhandsontable(df,stretchH="all")
+ })
## output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
- ## if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all") else NULL
+ ## if (nrow(rvTab$mzML) !=0) rhandsontable::rhandsontable(rvTab$mzML,stretchH="all") else NULL
## })
## output$nvPanel<-shiny::renderUI({
## message("Rendering panel started")
- ## ft<-rvConf$fTab
+ ## ft<-rvTab$mtr
## set<-input$presSelSet
## if (nchar(set)>0 && !is.null(ft)) {
## QANms<-rvConf$QANAMES