mkUI <- function(idSliderRange,setName,rtRange,tags,QANms) {
names(QANms) <- QANms
## Elements
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)
## 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))
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",
presHead,
shinydashboard::dashboardSidebar(width = 350,
shinydashboard::sidebarMenu(presMenuItem)),
shinydashboard::dashboardBody(shinydashboard::tabItems(presTabItem)))}
##' 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,
buttonTxt="Set",
txtTxt="",
icon="file",
...) {
shinydashboard::box(title=title,
shiny::textInput(txtName,NULL,value=txtTxt),
shinyFiles::shinyFilesButton(buttonName,
label=buttonTxt,
title=buttonTxt,
icon=shiny::icon(icon),
multiple=T),
solidHeader=T,
collapsible=F,...)}
confCompFnBrowse <- browseFile(title="Compound table file",
txtName="compListInp",
buttonName="compListB",
width=NULL)
confmzMLSets <- shinydashboard::box(title="Sets and tags",
shiny::textInput("setPropInp",
"What is a set?",
value=""),
shiny::textInput("setsInp",
"Comma-delimited list of set types",
value=""),
shiny::textInput("tagPropInp",
"What is a tag?",
value=""),
shiny::textInput("tagsInp",
"Comma-delimited list of tag types",
value=""),
width=NULL)
confState <- shinydashboard::box(title="Configuration state",
shinyFiles::shinySaveButton("saveConfB",
"Save configuration",
title="Save",
filename = "conf-state.rds",
"rds"),
shinyFiles::shinySaveButton("restoreConfB",
label="Restore configuration",
title="Restore",
filename= "",
"rds"),
width=NULL)
confLayout <- shiny::fluidRow(shiny::column(confCompFnBrowse,
confmzMLSets,
confState,
width=4),
shiny::column(width=8,
shinydashboard::box(title="mzML file table",
shinyFiles::shinyFilesButton("mzMLB",
label="Select mzML files",
title="Select mzML files",
icon=shiny::icon("files"),
multiple=T),
rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
width=NULL)))
headerText <- "Shinyscreen"
confSideItem <- shinydashboard::menuItem(text="Config",
tabName="config",
icon=shiny::icon("dashboard"))
compListSideItem <- shinydashboard::menuItem(text="Compound List",
tabName="compList",
icon=shiny::icon("dashboard"))
presSideItem <- shinydashboard::menuItem(text="Prescreening",
tabName="prescreen",
icon=shiny::icon("dashboard"))
header <- shinydashboard::dashboardHeader(title=headerText)
sidebar <- shinydashboard::dashboardSidebar(confSideItem,
compListSideItem,
presSideItem)
confTab <- shinydashboard::tabItem(tabName="config",
shiny::h2("Config"),
confLayout)
compListTab <- shinydashboard::tabItem(tabName="compList",shiny::h2("Compound Table"))
presTab <- shinydashboard::tabItem(tabName="prescreen",shiny::h2("Prescreening"))
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(confTab,
compListTab,
presTab))
shinydashboard::dashboardPage(header,
sidebar,
body)}
##' @export
shinyScreenApp <- function() {
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=character(),
tag=character(),
stringsAsFactors=F)
res
}
extd_mzMLtab<-function(ft,fn) {
modeLvl<- c("select","pH","pNa","pM",
"mH","mFA")
lSet<-levels(ft$set)
lTag<-levels(ft$tag)
newRow<-data.frame(Files=fn,
mode=factor(modeLvl[[1]],levels=modeLvl),
set=if (! is.null(lSet)) factor(lSet[[1]],levels=lSet) else "",
tag=if (! is.null(lTag)) factor(lTag[[1]],levels=lTag) else "",
stringsAsFactors = F)
levels(newRow$mode)<-modeLvl
res<-rbind(ft,newRow,
stringsAsFactors = F,
make.row.names = F)
levels(res$mode)<-modeLvl
res
}
server <- function(input,output,session) {
rvConf <- shiny::reactiveValues(mzMLtab=mk_mzMLtab(),
tags=list(),
sets=list(),
compListFn="",
tagProp="",
setProp="",
mode=modeLvl)
shinyFiles::shinyFileChoose(input, 'compListB',root=volumes)
shinyFiles::shinyFileChoose(input, 'mzMLB',root=volumes)
shinyFiles::shinyFileSave(input, 'saveConfB',root=volumes)
shinyFiles::shinyFileSave(input, 'restoreConfB',root=volumes)
getTags<-shiny::reactive({
if (length(input$tagsInp)>0 && !is.na(input$tagsInp)) unlist(strsplit(input$tagsInp, ",")) else list()
})
getSets<-shiny::reactive({
if (length(input$setsInp)>0 && !is.na(input$setsInp)) unlist(strsplit(input$setsInp, ",")) else list()
})
update_setstags_mzMLtab<-shiny::reactive({
tags<-getTags()
sets<-getSets()
message("+++++++++++++++++")
message("tags:",str(tags))
message("-----------------")
message("sets:",str(sets))
message("=================")
tagCol<-rvConf$mzMLtab$tag
setCol<-rvConf$mzMLtab$set
if (length(levels(tagCol))==0) rvConf$mzMLtab$tag<-factor(tagCol)
if (length(levels(setCol))==0) rvConf$mzMLtab$set<-factor(setCol)
rvConf$mzMLtab$tag<-factor(tagCol,levels=tags)
rvConf$mzMLtab$set<-factor(setCol,levels=sets)
})
## shiny::observe({
## input$saveConfB
## fn<-shinyFiles::parseSavePath(root=volumes,input$saveConfB)[["datapath"]]
## if ((! is.null(fn)) && length(fn)>0) {
## sav<-list()
## shiny::isolate(for (nm in names(rvConf)) {
## sav[[nm]]<-rvConf[[nm]]
## })
## saveRDS(object=sav,file=fn)
## }
## })
## shiny::observe({
## input$restoreConfB
## fn<-shinyFiles::parseSavePath(root=volumes,input$restoreConfB)[["datapath"]]
## if ((! is.null(fn)) && length(fn)>0) {
## lod<-readRDS(fn)
## for (nm in names(lod)) {
## rvConf[[nm]]<-lod[[nm]]
## }
## sets<-levels(rvConf$mzMLtab$set)
## tags<-levels(rvConf$mzMLtab$tag)
## if (!is.null(sets)) {
## thing<-do.call(paste,
## c(as.list(sets),
## list(sep=',')))
## shiny::updateTextInput(session=session,
## inputId="setsInp",
## value=thing)
## }
## if (!is.null(tags)) {
## thing<-do.call(paste,
## c(as.list(tags),
## list(sep=',')))
## shiny::updateTextInput(session=session,
## inputId="tagsInp",
## value=thing)
## }
## shiny::isolate({
## shiny::updateTextInput(session=session,
## inputId="setPropInp",
## value=rvConf$setProp)
## shiny::updateTextInput(session=session,
## inputId="tagPropInp",
## value=rvConf$tagProp)
## shiny::updateTextInput(session=session, #FIXME: this does not update right.
## inputId = "compListInp",
## value=rvConf$compListFn)})
## }
## })
shiny::observe({
input$compListB
res<-shinyFiles::parseFilePaths(root=volumes,input$compListB)
rvConf$compListFn<-res[["datapath"]]
shiny::updateTextInput(session=session,
inputId = "compListInp",
value=rvConf$compListFn)
})
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)
}
})
})
output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
rvConf$mzMLtab
update_setstags_mzMLtab()
if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all")
})
session$onSessionEnded(function () stopApp())
}
shiny::shinyApp(ui=mkUI2(),server=server)
}