-
Todor Kondic authoredTodor Kondic authored
Code owners
Assign users and groups as approvers for specific file changes. Learn more.
shinyUI.R 50.17 KiB
mkUI <- function() {
browseFile <- function(title,
buttonName,
txtName,
buttonTxt="Import compound list.",
txtTxt="",
icon="file",
description=NULL,
...) {
shinydashboard::box(title=title,
shiny::h5(description),
,
solidHeader=T,
collapsible=F,...)}
confImport <- shinydashboard::box(title="Import",
shiny::h5("There are two tables that need to be supplied before prescreening starts. One is the compound list, its format being the same like the one for the RMassBank (fields: ID,Name,SMILES,RT,CAS,mz,Level). Another is the compound set table (fields: ID,set). Once those tables are imported, they can further be modified as copies inside the project dir. Shinyscreen will never modify any initial (meta)data. If set field of the compound set table is NA, then that file is in a set of its own. The table format should be CSV with `,' as delimiter and any strings that possibly contain commas should be protected. LibreOffice Calc is helpful when it is needed to convert CSVs from one format to another, as well as protecting strings with quotes. "),
shiny::textInput("impCmpListInp",
"Imported compound list.",
value=""),
shiny::textInput("impSetIdInp",
"Compound set table.",
value=""),
shiny::textInput("impGenRMBInp",
"RMassBank settings.",
value=""),
shinyFiles::shinyFilesButton("impCmpListB",
label="Import compound list.",
title="",
icon=shiny::icon("file"),
multiple=F),
shinyFiles::shinyFilesButton("impSetIdB",
label="Import compound set table.",
title="",
icon=shiny::icon("file"),
multiple=T),
shinyFiles::shinyFilesButton("impGenRMBB",
label="Import RMassBank settings.",
title="",
icon=shiny::icon("file"),
multiple=F),
width=NULL)
confmzMLTags <- shinydashboard::box(title="Sets and Tags",
shiny::h5("Shinyscreen uses two properties, tags and sets, to categorise mzML data. Tags are properties of individual files. For example, if a single file represents a collection of spectra acquired at a specific collision energy, that energy could be used as a tag. Tags are used to differentiate the spectra in a chromatogram. Sets are collections of tagged files and are read from the compound set table. Each set is going to be screened for a designated collection of masses."),
shiny::textInput("tagPropInp",
"What is a tag? (example: collision energy; can be left empty.)",
value=""),
shiny::textInput("tagsInp",
"Comma-delimited list of tag types",
value=""),
width=NULL)
confState <- shinydashboard::box(title="Configuration state",
shiny::h5("Saves and restores current configuration."),
shinyFiles::shinySaveButton("saveConfB",
"Save configuration",
title="Save",
filename = "conf-state.rds",
"rds"),
shinyFiles::shinyFilesButton("restoreConfB",
label="Restore configuration",
multiple=F,
title="Restore"),
width=NULL)
confPP<-shinydashboard::box(title="Preprocessing settings",
shiny::textInput("confFileTabBase",
"Basic file table.", value=FN_FTAB_BASE),
shiny::textInput("confFileTabProcInp",
"Preprocessed file table.",
value=FN_FTAB_PP),
shiny::textInput("confResFileTab",
"Resulting file table.",
value=FN_FTAB),
width=NULL)
confmzMLtab <-shinydashboard::box(title="mzML file table",
shiny::h5("Use this file table to assign adduct modes and tags to the data files."),
shinyFiles::shinyFilesButton("mzMLB",
label="Select mzML files",
title="Select mzML files",
icon=shiny::icon("files-o"),
multiple=T),
shiny::actionButton("mzMLtabSubmB",
label="Submit mzML list.",
icon=shiny::icon("check")),
rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
width=NULL)
confLayout <- shiny::fluidRow(shiny::column(confImport,
confmzMLTags,
confState,
width=4),
shiny::column(width=8,
confPP,
confmzMLtab))
confTab <- shinydashboard::tabItem(tabName="config",
confLayout)
## ***** Compound List Tab *****
cmpListBox<-shinydashboard::box(title="Compound list",
rhandsontable::rHandsontableOutput("cmpListCtrl"),
width=NULL)
cmpListLayout <- shiny::fluidRow(shiny::column(cmpListBox,
width = 12))
cmpListTab <- shinydashboard::tabItem(tabName="compList",
shiny::h5("This is an editable view of the compound list."),
cmpListLayout)
## ***** Sets of compounds *****
setIdBox<-shinydashboard::box(title="Compound sets",
rhandsontable::rHandsontableOutput("setIdTabCtrl"),
width = NULL)
setIdLayout<-shiny::fluidRow(shiny::column(setIdBox,
width = 12))
setIdTab<-shinydashboard::tabItem(tabName="setId",
shiny::h5("This is an editable view of the id/set list."),
setIdLayout)
genBoxParam1<-shinydashboard::box(title="Parameters of the run",
shiny::textInput("genNoProc",
label="Number of processes.",
value=1),
shiny::textInput("ppmLimFine",
label="ppm limit fine",
value=10),
shiny::textInput("eicLim",
label="EIC limit.", value=1e-3),
shiny::textInput("intTresh",
label="Intensity threshold.",
value=1e5),
shiny::textInput("noiseFac",
label="Signal-to-noise ratio.",
value=3),
shiny::textInput("rtDelta",
label="Retention time Δ",
value=0.5),
width=NULL)
genBoxParam2<-shinydashboard::box(title=NULL,
shiny::selectInput("genSetSelInp",
label="Select set(s).",
choices="",
multiple=T),
shiny::actionButton(inputId="genRunB",
label="Run!",
icon=shiny::icon("bomb")),
width=NULL)
genBoxProcessed<-shinydashboard::box(title="Processed sets",
shiny::actionButton(inputId="genFileTabB",
label="Generate file table.",
icon=shiny::icon("save")),
shiny::actionButton(inputId="genRunPPB",
label="Preprocess!",
icon=shiny::icon("bomb")),
rhandsontable::rHandsontableOutput("genTabProcCtrl"),
width=NULL)
genTab<-shinydashboard::tabItem(tabName = "gen",
shiny::h5("Prepare for prescreening."),
shiny::fluidRow(shiny::column(genBoxProcessed,
width=4)),
shiny::fluidRow(shiny::column(genBoxParam1,width=4)),
shiny::fluidRow(shiny::column(genBoxParam2,width=4)))
## ***** Prescreening *****
## Prescreening elements
preshead <- shinydashboard::dashboardHeader(title = "Prescreening")
presCompInfo <- shiny::fluidRow(shinydashboard::box(title = "MS Prescreening",
width = 7,
height = "80px",
background = "blue",
""),
shinydashboard::box(title = "Compound ID N°",
width = 5,
height = "80px",
background = "olive",
shiny::textOutput("compoundID")))
presPlotBox <- shinydashboard::box(title = "Plot",
width = 7,color = "olive",
solidHeader = FALSE,
collapsible = TRUE,
shiny::plotOutput("chromGram",
width = "100%",
height = "750px",
click = NULL,
dblclick = NULL,
hover = NULL,
hoverDelay = NULL,
hoverDelayType = NULL,
brush = NULL,
clickId = NULL, hoverId = NULL),
shiny::textInput("plotname",
"Insert plot name: (e.g. plotname_%i.pdf)",
value="plotCpdID_%i.pdf"),
shiny::actionButton("saveplot",
"Save",
icon = shiny::icon("save")),
shiny::actionButton("saveallplots",
"Save All Plots",
icon = shiny::icon("save")))
presCompSelBox <- shinydashboard::box(title = "Compounds",
width=5,
solidHeader = FALSE,
color = "olive",
collapsible = TRUE,
"",
shiny::br(),
shiny::selectInput("presSelSet",
"Set",
choices="",
multiple=F),
shiny::actionButton("presPrev",
"Previous compound.",
icon = shiny::icon("backward")),
shiny::actionButton("presNext",
"Next compound.",
icon = shiny::icon("forward")),
shiny::selectInput("presSelCmpd",
"Compound",
choices="",
multiple=F))
nvPanel<-shiny::uiOutput("nvPanel")
presQABox <- shinydashboard::box(title = "Prescreening analysis",
width = 5,
solidHeader = FALSE,
collapsible = TRUE,
nvPanel,
shiny::actionButton("submitQA",
"Submit",
icon = shiny::icon("save")),
shiny::textInput("fn_ftable",
"File table Name",
value=FN_FTAB),
shiny::actionButton("savefiletable",
"Save File Table",
icon = shiny::icon("save")))
presPlotParBox <- shinydashboard::box(title = "Plot Parameters",
width=7,
solidHeader = FALSE,
collapsible = TRUE,
"",
shiny::br(),
shiny::numericInput("min_val",
"Minimum x Axis Value",
DEFAULT_RT_RANGE[[1]]),
shiny::numericInput("max_val",
"Maximum x Axis Value",
DEFAULT_RT_RANGE[[2]]),
shiny::radioButtons("yaxis",
"Parameters for y Axis",
c(linear = "linear",
log = "log")),
shiny::numericInput("nice",
"Nice",
DEFAULT_RT_RANGE[[1]]),
shiny::numericInput("steps",
"Steps",
DEFAULT_RT_RANGE[[2]])) presPlotWidget <- shiny::fluidRow(presPlotBox,
presCompSelBox,
presQABox,
presPlotParBox)
presTab <- shinydashboard::tabItem(tabName = "prescreen",
shiny::h2("Prescreening"),
presCompInfo,
presPlotWidget)
## ***** Top-level Elements *****
headerText <- "Shinyscreen"
confSideItem <- shinydashboard::menuItem(text="Config",
tabName="config",
icon=shiny::icon("user-cog"))
compListSideItem <- shinydashboard::menuItem(text="Compound list",
tabName="compList",
icon=shiny::icon("table"))
setIdSideItem <- shinydashboard::menuItem(text="Compound sets",
tabName="setId",
icon=shiny::icon("table"))
genSideItem <- shinydashboard::menuItem(text="Generate prescreen data",
tabName="gen",
icon=shiny::icon("cogs"))
presSideItem <- shinydashboard::menuItem(text="Prescreening",
tabName="prescreen",
icon=shiny::icon("chart-bar"))
header <- shinydashboard::dashboardHeader(title=headerText)
sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(confSideItem,
compListSideItem,
setIdSideItem,
genSideItem,
presSideItem))
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(confTab,
cmpListTab,
setIdTab,
genTab,
presTab))
shinydashboard::dashboardPage(header,
sidebar,
body)}
##' @export
shinyScreenApp <- function(projDir=getwd()) {
message("projDir=",projDir)
modeLvl<- c("pH","pNa","pM",
"mH","mFA")
volumes <- shinyFiles::getVolumes()
mk_mzMLtab<-function() {
modeLvl<- c("pH","pNa","pM", "mH","mFA")
res<-data.frame(Files=character(),
mode=factor(levels=modeLvl),
set=factor(),
tag=factor(),
stringsAsFactors=F)
res
}
mk_cmpList<-function() {
data.frame(ID=integer(),
Name=character(),
SMILES=character(),
RT=double(),
CAS=character(),
stringsAsFactors = F)
}
mk_setId<-function() {
data.frame(ID=integer(),
set=character())}
extd_mzMLtab<-function(ft,fn) {
modeLvl<- c("select","pH","pNa","pM",
"mH","mFA")
lSet<-levels(ft$set)
lTag<-levels(ft$tag)
newRow<-data.frame(Files=fn,
mode=factor(modeLvl[[1]],levels=modeLvl),
set=if (length(lSet) > 0) factor(lSet[[1]],levels=lSet) else factor("unspecified"),
tag=if (length(lTag) > 0) factor(lTag[[1]],levels=lTag) else factor("unspecified"),
stringsAsFactors = F)
levels(newRow$mode)<-modeLvl
res<-rbind(ft,newRow,
stringsAsFactors = F,
make.row.names = F)
levels(res$mode)<-modeLvl
res
}
readSetId<-function(fn) {
read.csv(file=fn,
header=T,
stringsAsFactors = T,
comment.char = '',
na.strings = c("","NA"))
}
getMz<-function(ids,cmpdL) {
mz<-sapply(ids,function(i) {mzs<-cmpdL$mz[cmpdL$ID==i]
if (length(mzs)>1) mzs[[1]] else mzs
})
names(mz)<-NULL
mz
}
mkCmpdDrop<-function(set,setTab) {
wh<-which(setTab$set %in% set)
ids<-setTab$ID[wh]
mz<-setTab$mz[wh]
entries<-base::Map(function(i,m) paste(i,'; ','mz: ',m,sep=''),ids,mz)
entries
}
queryFileTable <- function(df,set,id) { df[(df$ID %in% id) & (df$set %in% set),]
}
updateFileTable <- function(df,set,id,linput) {
for (tag in names(linput)) {
entries <- names(linput[[tag]])
cond <- (df$ID %in% id) & (df$tag == tag) & (df$set %in% set)
df[cond,entries] <- linput[[tag]]
}
df
}
getCheckboxValues <- function(tag,input,rv) {
chkbox <- input[[rv$spectProps[[tag]]]]
q <- sapply(QANAMES,function (qn) if (qn %in% chkbox) T else F)
names(q) <- QANAMES
q
}
server <- function(input,output,session) {
## ***** reactive values *****
rvConf <- shiny::reactiveValues(mzMLtab=mk_mzMLtab(),
tags=list(),
sets=list(),
spectProps=list(),
QANAMES=QANAMES,
MODEMAP=MODEMAP,
impCmpListFn="",
impSetIdFn="",
impGenRMBFn="",
fnLocSetId=FN_LOC_SETID,
fnFTBase="",
tagProp="",
setProp="",
mode=modeLvl,
projDir=projDir,
currSet=NA,
currIDSel=1,
currIDSet=list(),
currID=NA,
fnFT=NULL,
fTab=NULL)
rvCmpList<- shiny::reactiveValues(df=mk_cmpList())
rvSetId<- shiny::reactiveValues(df=mk_setId())
rvPres<-shiny::reactiveValues(cex=CEX,
rt_digits=RT_DIGITS,
m_digits=M_DIGITS,
pal=PAL,
plot_id=NULL)
## ***** shinyFiles observers *****
wdroot<-c(wd=projDir)
shinyFiles::shinyFileChoose(input, 'impCmpListB',roots=volumes)
shinyFiles::shinyFileChoose(input, 'impSetIdB',roots=volumes)
shinyFiles::shinyFileChoose(input, 'impGenRMBB',roots=volumes)
shinyFiles::shinyFileSave(input, 'saveConfB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'restoreConfB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'mzMLB',roots=volumes)
## ***** reactive function definitions *****
getTags<-shiny::reactive({
if (length(input$tagsInp)>0 && !is.na(input$tagsInp)) unlist(strsplit(input$tagsInp, ",")) else list()
})
getSets<-shiny::reactive({
levels(rvSetId$df$set)
})
getCmpL<-shiny::reactive({
rvCmpList$df #rhandsontable::hot_to_r(input$cmpListCtrl)
})
getSetId<-shiny::reactive({
rvSetId$df #rhandsontable::hot_to_r(input$setIdTabCtrl)
})
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$tag<-factor(tagCol,levels=tags)
})
update_sets_mzMLtab<-shiny::reactive({
sets<-getSets()
setCol<-rvConf$mzMLtab$set
if (length(levels(setCol))==0) rvConf$mzMLtab$set<-factor(setCol)
rvConf$mzMLtab$set<-factor(setCol,levels=sets)
})
saveConf<-reactive({
fn<-shinyFiles::parseSavePath(root=c(wd=rvConf$projDir),input$saveConfB)[["datapath"]]
if ((! is.na(fn)) && length(fn)>0) {
message("Saving config to",fn)
sav<-list()
sav<-list(rvConf=list(),
input=list())
shiny::isolate(for (nm in names(rvConf)) {
sav$rvConf[[nm]]<-rvConf[[nm]]
})
sav$input$tagsInp<-input$tagsInp
sav$input$setsInp<-input$setsInp
sav$input$impCmpListInp<-input$impCmpListInp
sav$input$impSetIdInp<-input$impSetIdInp
sav$input$impGenRMBInp<-input$impGenRMBInp
saveRDS(object=sav,file=fn)
}
})
restoreConf<-reactive({
input$restoreConfB
fnobj<-shinyFiles::parseFilePaths(root=c(wd=rvConf$projDir),input$restoreConfB)
fn<-fnobj[["datapath"]]
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$mzMLtab
rvConf$fnFTBase<-sav$rvConf$fnFTBase
rvConf$fnFT<-sav$rvConf$fnFT
}
})
currSetMkCmpMenu<-shiny::reactive({
set<-rvConf$currSet
setID<-getSetId()
hasMz<-"mz" %in% colnames(setID)
if (!is.na(set) && hasMz) {
setID<-setID[setID$set %in% set,]
ids<-setID$ID[set %in% setID$set]
entries<-mkCmpdDrop(set,setID)
ch<-as.list(1:length(ids))
names(ch)<-entries
shiny::updateSelectInput(session=session,
"presSelCmpd",
choices=ch,
selected = 1)
rvConf$currIDSet<-ids
}
})
currSetPreCalc<-shiny::reactive({
set<-rvConf$currSet
fTab<-rvConf$fTab
if (!is.na(set) && length(fTab)>0) {
setId<-getSetId()
hasMz<-"mz" %in% colnames(setId)
if (hasMz) {
setIdIds<-setId[,"ID"]
setIdSMILES<-setId[,"SMILES"]
setIdMz<-setId[,"mz"]
tags<-rvConf$tags
iSet<-which(set==fTab$set)
sfTab<-fTab[iSet,]
tags<-levels(factor(sfTab$tag))
iTag<- match(tags,sfTab$tag)
wd<-sfTab$wd[iTag]
cmpL<-rvCmpList$df
preID<-setIdIds
smiles<-setIdSMILES
mz<-setIdMz
names(smiles)<-as.character(preID)
names(mz)<-as.character(preID)
## Get the basenames of eic files.
eics <- list.files(path=wd[[1]],patt=".*eic.csv")
eicsPref <- sapply(strsplit(eics,split="\\."),function(x) x[[1]])
eicsID <- as.integer(eicsPref)
maybekids <- sapply(eicsPref,function(x) {paste(x,'.kids.csv',sep='')})
names(eics) <- eicsID names(maybekids) <- eicsID
plot_id <- function (i,rtrange=NULL,log=input$yaxis) {
i=as.character(i)
mz=mz[[i]]
smile<-smiles[[i]]
message("i:",i)
message("mz:",mz)
message("smile:",smile)
plot_id_aux(i,wd=wd,eics=eics,maybekids=maybekids,mass=mz,smile=smile,tags=tags,log=log,rtrange=rtrange,cex=rvPres$cex,pal=rvPres$pal,rt_digits=rvPres$rt_digits,m_digits=rvPres$m_digits,fTab=sfTab)
}
rvPres$plot_id<-plot_id
}
}
})
## ***** Observe Event *****
shiny::observeEvent(input$saveConfB,{
saveConf()
})
shiny::observeEvent(input$impSetIdB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impSetIdB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impSetIdInp",
value=fn)
}})
shiny::observeEvent(input$impCmpListB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impCmpListB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impCmpListInp",
value=fn)
}})
shiny::observeEvent(input$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$df)
mode<-rvConf$mzMLtab
dfSet<-rvSetId$df
dfSet$mz<-rep(NA,nR)
dfSet$SMILES<-rep(NA,nR)
cmpL<-getCmpL()
for (s in sets) {
md<-setMode[[s]]
ind<-which(dfSet$set==s)
for (i in ind) {
id<-dfSet[i,"ID"]
dfSet[i,"mz"]<-getMzFromCmpL(id,md,cmpL)
dfSet[i,"SMILES"]<-getSMILESFromCmpL(id,cmpL)
}
}
## 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$impGenRMBB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impGenRMBInp",
value=fn)
}})
shiny::observeEvent(input$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(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$genRunPPB,{
message("Starting preprocessing.")
shiny::isolate({
sets<-getSets()
cdf<-if (!is.null(rvCmpList$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.")
}
}
}
})
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$currIDSel<-x
})
shiny::observeEvent(input$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$currIDSel,{
ids<-rvConf$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$currID,
linput=res)
})
shiny::observeEvent(input$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$yaxis)
dev.off()
message("Plotting compound ", i," to ",fn," done.")
})
shiny::observeEvent(input$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$genTabProcCtrl<-rhandsontable::renderRHandsontable({
sets<-getSets()
genState<-sapply(sets,isGenDone)
df<-if (!is.null(sets)) {data.frame(set=sets,
generated=genState,
stringsAsFactors=F)
} else {data.frame(sets=character(),
generated=logical(),
stringsAsFactors=F)}
rhandsontable::rhandsontable(df,
rowHeaders=NULL,
readOnly=T,
stretchH="all")
}) })
shiny::observe({
shiny::invalidateLater(100,
session=session)
fnFT<-if (file.exists(input$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({
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({
message("currSet START")
currSetMkCmpMenu()
currSetPreCalc()
message("currSet END")
})
shiny::observe({
input$restoreConfB
message("Restore event observed.")
restoreConf()
message("Restore event finished.")
})
## shiny::observe({
## rvConf$tags<-getTags()
## })
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)
})
})
## ***** 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$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
if (nrow(rvConf$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$spectProps<-spectProps
tabPanelList <- lapply(tags, function(tag) {
shiny::tabPanel(tag, shiny::checkboxGroupInput(spectProps[[tag]], "Quality Control",
QANms),
shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
shiny::verbatimTextOutput(paste("value",tag,sep=""))
)})
do.call(shiny::navlistPanel, tabPanelList)
message("done rendering panel")
} else NULL
})
output$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$yaxis)
}
})
session$onSessionEnded(function () stopApp())
}
shiny::shinyApp(ui=mkUI(),server=server)
}