Newer
Older
mkUI <- function(idSliderRange,setName,rtRange,tags,QANms) {
names(QANms) <- QANms
tabPanelList <- lapply(tags, function(tag) {
shiny::tabPanel(tag, shiny::checkboxGroupInput(paste("spectProps",tag,sep=""), "Quality Control",
QANms),
shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
shiny::verbatimTextOutput(paste("value",tag,sep=""))
)})
nvPanel <- do.call(shiny::navlistPanel, tabPanelList)
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## Prescreening elements
preshead <- shinydashboard::dashboardHeader(title = "Prescreening")
presMenuItem <- shinydashboard::menuItem(text = "The Prescreening",
tabName = "Prescreen",
icon = shiny::icon("dashboard"))
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("plot1",
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::sliderInput("idslider",
"Compound number:",
idSliderRange[1],
idSliderRange[2],
value=1,
step=1))
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presQABox <- shinydashboard::box(title = "Prescreening analysis",
width = 5,
solidHeader = FALSE,
collapsible = TRUE,
shiny::titlePanel(setName),
nvPanel,
shiny::actionButton("submitQA",
"Submit",
icon = shiny::icon("save")),
shiny::textInput("fn_ftable",
"File table Name",
value="ftable.csv"),
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",
rtRange[1]),
shiny::numericInput("max_val",
"Maximum x Axis Value",
rtRange[2]),
shiny::radioButtons("yaxis",
"Parameters for y Axis",
c(linear = "linear",
log = "log")),
shiny::numericInput("nice",
"Nice",
rtRange[1]),
shiny::numericInput("steps",
"Steps",
rtRange[2]))
presPlotWidget <- shiny::fluidRow(presPlotBox,
presCompSelBox,
presQABox,
presPlotParBox)
presTabItem <- shinydashboard::tabItem(tabName = "Prescreen",
shiny::h2("The Prescreen plot"),
presCompInfo,
presPlotWidget)
## Assemble the UI.
ui <- shinydashboard::dashboardPage(skin="black",
shinydashboard::dashboardSidebar(width = 350,
shinydashboard::sidebarMenu(presMenuItem)),
shinydashboard::dashboardBody(shinydashboard::tabItems(presTabItem)))}
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##' Prescreening using shiny interface.
##'
##' @title Prescreening with Shiny
##' @return Nothing useful.
##' @author Jessy Krier
##' @author Mira Narayanan
##' @author Hiba Mohammed Taha
##' @author Anjana Elapavalore
##' @author Todor Kondić
##' @param prescdf File table data-frame. Columns: Files,ID,wd,tag,set_name ...
##' @param mode RMassBank mode.
##' @param fn_cmpd_l Compound list file name.
##' @param pal ColorBrewer palette.
##' @param cex Size of fonts.
##' @param rt_digits Number of decimal places for the retention time.
##' @param m_digits Number of decimal places for the mass.
##' @export
presc.shiny <-function(prescdf=NULL,mode=NULL,fn_cmpd_l=NULL,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
## Helper functions
queryFileTable <- function(df,id) {
df[df$ID %in% id,]
}
updateFileTable <- function(df,id,linput) {
for (tag in names(linput)) {
entries <- names(linput[[tag]])
cond <- (df$ID %in% id) & (df$tag == tag)
df[cond,entries] <- linput[[tag]]
}
df
}
## Constants
MODEMAP=list(pH="MpHp_mass",
mH="MmHm_mass",
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
DEFAULT_RT_RANGE=c(NA,NA)
QANAMES <- c("MS1","MS2","Alignment","AboveNoise")
prescdf$tag <- as.character(prescdf$tag)
tags <- levels(factor(prescdf$tag))
wd <- prescdf$wd[match(tags,prescdf$tag)]
wd1 <- wd[[1]]
cmpd_l_df <- read.csv(file=fn_cmpd_l,stringsAsFactors = F,comment.char='')
preID <- as.integer(levels(factor(prescdf$ID)))
selID <- which(cmpd_l_df$ID %in% preID)
osmesi <- cmpd_l_df$SMILES[selID]
no_cmpds <- length(preID)
# reconf(wd1)
masses <- lapply(osmesi,function (smile) {
#osmesi <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
zz <- RChemMass::getSuspectFormulaMass(smile)
zz[[MODEMAP[[mode]]]]
})
names(osmesi) <- as.character(preID)
names(masses) <- as.character(preID)
## Get the basenames of eic files.
eics <- list.files(path=wd[[1]],patt=".*eic.csv")
eicsPref <- sapply(strsplit(eics,split="\\."),function(x) x[[1]])
eicsID <- as.integer(eicsPref)
maybekids <- sapply(eicsPref,function(x) {paste(x,'.kids.csv',sep='')})
names(eics) <- eicsID
names(maybekids) <- eicsID
plot_id <- function (i,rtrange=NULL,log=rv$yaxis) plot_id_aux(i=as.character(i),wd=wd,eics=eics,maybekids=maybekids,mass=masses[[as.character(i)]],smile=osmesi[[as.character(i)]],tags=tags,log=log,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits,fTab=prescdf)
spectProps <- sapply(tags,function (tag) paste("spectProps",tag,sep=""))
idSliderRange <- c(1,length(preID))
ui <- mkUI(idSliderRange=idSliderRange,setName=prescdf$set_name,rtRange=DEFAULT_RT_RANGE,tags=tags,QANms=QANAMES)
getCheckboxValues <- function(tag,input) {
chkbox <- input[[spectProps[[tag]]]]
q <- sapply(QANAMES,function (qn) if (qn %in% chkbox) T else F)
names(q) <- QANAMES
q
}
server <- function(input, output, session) {
rv <- shiny::reactiveValues(prescList=list(),
prescdf=prescdf,
spectProps=spectProps,
tags=tags,
default_range=DEFAULT_RT_RANGE,
no_cmpds=no_cmpds)
output$plot1 <- renderPlot(
{
i=preID[[input$idslider]]
rtrange <- c(input$min_val,input$max_val)
plot_id(i,rtrange=rtrange, log=input$yaxis)
# intParameter <- c(input$nice, input$steps)
})
output$value <- renderText(
{
input$caption
})
output$compoundID <- renderText(
{
preID[[input$idslider]]
})
shiny::observeEvent(input$saveplot,
{
i=preID[[input$idslider]]
pfn <-input$plotname
if (is.na(pfn)) pfn <- "plotCpdID_%i.pdf"
fn <- sprintf(pfn,i)
rtrange <- c(input$min_val,input$max_val)
pdf(file=fn, width=12, height=8)
plot_id(i,rtrange=rtrange, log=input$yaxis)
dev.off()
})
shiny::observeEvent(input$saveallplots,
{
i=preID[[input$idslider]]
pfn <-input$plotname
if (is.na(pfn)) pfn <- "plotall.pdf"
fn <- sprintf(pfn,i)
pdf(file=fn, width=12, height=8)
for (i in preID) {
plot_id(i,log=input$yaxis)
message("Compound ID ",i," done.")
}
dev.off()
})
shiny::observeEvent(input$submitQA,{
res <- lapply(rv$tags,getCheckboxValues,input)
names(res) <- rv$tags
rv$prescdf <- updateFileTable(df=rv$prescdf,id=preID[[input$idslider]],linput=res)
})
shiny::observe({
i <- preID[[input$idslider]]
sdf <- queryFileTable(df=rv$prescdf,id=i)
for (t in sdf$tag) {
sprop <- rv$spectProps[[t]]
sel <- as.logical(sdf[sdf$tag %in% t,QANAMES])
choices <- QANAMES[sel]
names(choices) <- QANAMES[sel]
shiny::updateCheckboxGroupInput(session = session,inputId = sprop,selected=choices)
}
})
shiny::observeEvent(input$savefiletable,
{
write.csv(file=input$fn_ftable,x=rv$prescdf,row.names = F)
})
session$onSessionEnded(function() {
stopApp()
})
}
shiny::shinyApp(ui = ui, server = server)
}
mkUI2 <- function() {
browseFile <- function(title,
buttonName,
txtName,
txtTxt="",
icon="file",
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."),
shiny::textInput("impCmpListInp",
"Compound List",
value=""),
shinyFiles::shinyFilesButton("impCmpListB",
label="Import compound list.",
title="",
icon=shiny::icon("file"),
multiple=T),
shinyFiles::shinyFilesButton("impSetIdB",
label="Import compound set table.",
title="",
icon=shiny::icon("file"),
multiple=T),
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"),
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"),
multiple=T),
rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
width=NULL)
confLayout <- shiny::fluidRow(shiny::column(confImport,
confState,
width=4),
shiny::column(width=8,
confTab <- shinydashboard::tabItem(tabName="config",
confLayout)
## ***** Compound List Tab *****
cmpListBox<-shinydashboard::box(title="Compound list",
rhandsontable::rHandsontableOutput("cmpListCtrl"),
width=NULL)
cmpListState <- shinydashboard::box(title="Compound list state",
shinyFiles::shinySaveButton("saveCmpListB",
"Save",
title="Save",
filename = "compounds.csv",
"csv"),
shinyFiles::shinyFilesButton("restoreCmpListB",
label="Restore",
multiple=F,
title="Restore"),
width=NULL)
cmpListLayout <- shiny::fluidRow(shiny::column(cmpListState,
cmpListBox,
width = 12))
cmpListTab <- shinydashboard::tabItem(tabName="compList",
shiny::h5("This is an editable view of the compound list."),
## ***** Sets of compounds *****
setIdBox<-shinydashboard::box(title="Compound sets",
rhandsontable::rHandsontableOutput("setIdtabCtrl"),
width = NULL)
setIdBoxState<-shinydashboard::box(title="Compound list state",
shinyFiles::shinySaveButton("saveSetIdB",
"Save",
title="Save",
filename = "compound_sets.csv",
"csv"),
shinyFiles::shinyFilesButton("restoreSetIdB",
label="Restore",
multiple=F,
title="Restore"),
width=NULL)
setIdLayout<-shiny::fluidRow(shiny::column(setIdBoxState,
setIdBox,
width = 12))
setIdTab<-shinydashboard::tabItem(tabName="setId",
shiny::h5("This is an editable view of the id/set list."),
setIdLayout)
## ***** Prescreening *****
presTab <- shinydashboard::tabItem(tabName="prescreen")
headerText <- "Shinyscreen"
confSideItem <- shinydashboard::menuItem(text="Config",
tabName="config",
compListSideItem <- shinydashboard::menuItem(text="Compound List",
tabName="compList",
setIdSideItem <- shinydashboard::menuItem(text="Compound sets",
tabName="setId",
icon=shiny::icon("table"))
presSideItem <- shinydashboard::menuItem(text="Prescreening",
tabName="prescreen",
header <- shinydashboard::dashboardHeader(title=headerText)
sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(confSideItem,
compListSideItem,
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(confTab,
shinydashboard::dashboardPage(header,
sidebar,
body)}
##' @export
shinyScreenApp <- function() {
modeLvl<- c("pH","pNa","pM",
"mH","mFA")
mk_mzMLtab<-function() {
modeLvl<- c("pH","pNa","pM",
"mH","mFA")
res<-data.frame(Files=character(),
mode=factor(levels=modeLvl),
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())}
modeLvl<- c("select","pH","pNa","pM",
"mH","mFA")
lSet<-levels(ft$set)
lTag<-levels(ft$tag)
newRow<-data.frame(Files=fn,
mode=factor(modeLvl[[1]],levels=modeLvl),
set=if (! is.null(lSet)) factor(lSet[[1]],levels=lSet) else factor("unspecified"),
tag=if (! is.null(lTag)) factor(lTag[[1]],levels=lTag) else factor("unspecified"),
stringsAsFactors = F)
levels(newRow$mode)<-modeLvl
res<-rbind(ft,newRow,
stringsAsFactors = F,
make.row.names = F)
levels(res$mode)<-modeLvl
res
readCmpList<-function(fn) {
read.csv(file=fn,
header=T,
stringsAsFactors = F,
comment.char = '')
}
readSetId<-function(fn) {
read.csv(file=fn,
header=T,
stringsAsFactors = T,
comment.char = '',
na.strings = c("","NA"))
}
server <- function(input,output,session) {
rvConf <- shiny::reactiveValues(mzMLtab=mk_mzMLtab(),
tags=list(),
sets=list(),
tagProp="",
setProp="",
freshCmpListInp=F,
freshSetIdInp=F)
rvCmpList<- shiny::reactiveValues(df=mk_cmpList())
rvSetId<- shiny::reactiveValues(df=mk_setId())
## ***** shinyFiles observers *****
shinyFiles::shinyFileChoose(input, 'impCmpListB',root=volumes)
shinyFiles::shinyFileChoose(input, 'impSetIdB',root=volumes)
shinyFiles::shinyFileSave(input, 'saveConfB',root=volumes)
shinyFiles::shinyFileChoose(input, 'restoreConfB',root=volumes)
shinyFiles::shinyFileChoose(input, 'mzMLB',root=volumes)
shinyFiles::shinyFileSave(input, 'saveCmpListB',root=volumes)
shinyFiles::shinyFileChoose(input, 'restoreCmpListB',root=volumes)
shinyFiles::shinyFileSave(input, 'saveSetIdB',root=volumes)
shinyFiles::shinyFileChoose(input, 'restoreSetIdB',root=volumes)
## ***** reactive function definitions *****
getTags<-shiny::reactive({
if (length(input$tagsInp)>0 && !is.na(input$tagsInp)) unlist(strsplit(input$tagsInp, ",")) else list()
})
getSets<-shiny::reactive({
update_tags_mzMLtab<-shiny::reactive({
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=volumes,input$saveConfB)[["datapath"]]
if ((! is.na(fn)) && length(fn)>0) {
sav<-list()
sav<-list(rvConf=list(),
input=list())
shiny::isolate(for (nm in names(rvConf)) {
sav$rvConf[[nm]]<-rvConf[[nm]]
})
sav$input$tagsInp<-input$tagsInp
sav$input$setsInp<-input$setsInp
sav$input$impCmpListInp<-input$impCmpListInp
saveRDS(object=sav,file=fn)
}
})
restoreConf<-reactive({
fn<-shinyFiles::parseFilePaths(root=volumes,input$restoreConfB)[["datapath"]]
if ((! is.na(fn)) && length(fn)>0) {
sav<-readRDS(fn)
for (nm in names(sav$rvConf)) {
rvConf[[nm]]<-sav$rvConf[[nm]]
}
shiny::isolate({
shiny::updateTextInput(session=session,
inputId="tagsInp",
value=sav$input$tagsInp)
shiny::updateTextInput(session=session,
inputId="setsInp",
value=sav$input$setsInp)
shiny::updateTextInput(session=session,
inputId="impCmpListInp",
value=sav$input$impCmpListInp)
shiny::updateTextInput(session=session,
inputId="impCmpListInp",
value=sav$input$impCmpListInp)
getCmpListdf<-shiny::reactive({rvCmpList$df})
importCmpListdf<-shiny::reactive({
impCmpFn<-shinyFiles::parseFilePaths(root=volumes,
input$impCmpListB)[["datapath"]]
if (! (is.null(impCmpFn) || is.na(impCmpFn) || length(impCmpFn)==0)) {
message("Importing compound list from ",str(impCmpFn))
rvConf$impCmpListFn<-impCmpFn
rvConf$freshCmpListImp<-T
rvCmpList$df<-readCmpList(rvConf$impCmpListFn)
}
})
importSetIddf<-shiny::reactive({
impSetIdFn<-shinyFiles::parseFilePaths(root=volumes,
input$impSetIdB)[["datapath"]]
if (! (is.null(impSetIdFn) || is.na(impSetIdFn) || length(impSetIdFn)==0)) {
message("Importing setid table from ",str(impSetIdFn))
rvConf$impSetIdFn<-impSetIdFn
rvConf$freshSetIdImp<-T
rvSetId$df<-readSetId(rvConf$impSetIdFn)
}
})
## shiny::isolate({
## shiny::updateTextInput(session=session,
## inputId="setPropInp",
## value=rvConf$setProp)
## shiny::updateTextInput(session=session,
## inputId="tagPropInp",
## value=rvConf$tagProp)
shiny::observe({
input$mzMLB
fchoice<-shinyFiles::parseFilePaths(root=volumes,input$mzMLB)
paths<-fchoice[["datapath"]]
isolate({
for (pt in paths) {
rvConf$mzMLtab<-extd_mzMLtab(rvConf$mzMLtab,pt)
shiny::observe({
input$restoreConfB
restoreConf()
})
shiny::observe({
input$saveConfB
saveConf()
})
output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
update_tags_mzMLtab()
update_sets_mzMLtab()
if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all") else NULL
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shiny::observe({
shiny::updateTextInput(session=session,
inputId = "impCmpListInp",
value=rvConf$impCmpListFn)
})
## shiny::observeEvent(input$impCmpListB,
## {
## message("Here a")
## impCmpFn<-shinyFiles::parseFilePaths(root=volumes,
## input$impCmpListB)[["datapath"]]
## if (!is.null(impCmpFn) && !is.na(impCmpFn)) {
## message("Here b")
## shiny::isolate({
## rvConf$impCmpListFn<-impCmpFn
## rvConf$freshCmpListImp<-T
## rvCmpList$df<-readCmpList(rvConf$impCmpListFn)})
## message("New compound list import.")
## }
## })
output$cmpListCtrl <- rhandsontable::renderRHandsontable({
importCmpListdf()
df<-getCmpListdf()
if (rvConf$freshCmpListImp) {
shiny::isolate({
rvConf$freshCmpListImp<-F
})
}
rhandsontable::rhandsontable(df,stretchH="all")
})
output$setIdtabCtrl<- rhandsontable::renderRHandsontable({
importSetIddf()
df<-rvSetId$df
if (rvConf$freshSetIdInp) {
shiny::isolate({
rvConf$freshSetIdInp<-F
})
}
rhandsontable::rhandsontable(df,stretchH="all")
session$onSessionEnded(function () stopApp())
}
shiny::shinyApp(ui=mkUI2(),server=server)
}