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)
ui <- shinydashboard::dashboardPage(skin="black",
shinydashboard::dashboardHeader(title = "Prescreening"),
shinydashboard::dashboardSidebar(width = 350,
shinydashboard::sidebarMenu(shinydashboard::menuItem(text = "The Prescreening",
tabName = "Prescreen",
icon = shiny::icon("dashboard")))),
shinydashboard::dashboardBody(shinydashboard::tabItems(shinydashboard::tabItem(tabName = "Prescreen",
shiny::h2("The Prescreen plot"),
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"))),
shiny::fluidRow(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"))),
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)),
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"))),
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])))))))}
##' 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$set_name,rtRange=DEFAULT_RT_RANGE,tags=tags,QANms=QANAMES)
getCheckboxValues <- function(tag,input) {
chkbox <- input[[spectProps[[tag]]]]
q <- sapply(QANAMES,function (qn) if (qn %in% chkbox) T else F)
names(q) <- QANAMES
q
}
server <- function(input, output, session) {
rv_adduc<- shiny::reactiveValues(smiles=1,
resTable=1)
rv <- shiny::reactiveValues(prescList=list(),
prescdf=prescdf,
spectProps=spectProps,
tags=tags,
default_range=DEFAULT_RT_RANGE,
no_cmpds=no_cmpds)
output$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$smileslist,
{
rv_adduc$smiles <- read.csv(input$smileslist$datapath, header=FALSE,sep=',',stringsAsFactors=FALSE,comment.char = '')[[1]]
})
shiny::observeEvent(input$IdSmiles,
{
rv_adduc$smiles <- trimws(strsplit(input$IdSmiles,split="\n")[[1]],which="both")
})
output$masses <- renderTable(
{
legend <- list(MolForm="Formula",Monoiso_mass="Monoisotopic mass",MpHp_mass="[M+H]+","MpNH4_mass"="[M+NH4]+",MpNa_mass="[M+Na]+",MmHm_mass="[M-H]-")
expr =lapply(rv_adduc$smiles,function(smile) {
tryCatch(RChemMass::getSuspectFormulaMass(smile),
error=function(e) {message("getSuspectFormulaMass:",e);xx <- lapply(names(legend),
function (x) 0);names(xx) <- names(legend);xx$MolForm <- "ERROR";xx
},
warning=function(w) {message("getSuspectFormulaMass:",w);xx <- lapply(names(legend),
function (x) 0);names(xx) <- names(legend);xx$MolForm <- "ERROR";xx
})
})
if (! length(expr) == 0) {
df <- do.call(rbind,expr)
names(df) <- sapply(names(legend),function (nm) legend[[nm]],USE.NAMES=F)
df <- as.data.frame(df,stringsAsFactors=F)
names(df) <- sapply(names(legend),function (nm) legend[[nm]],USE.NAMES=F)
for (nm in names(df)) {
for (nr in 1:nrow(df)) {
if(df[nr,nm]=="error") df[nr,nm] <- NA
}
}
rv_adduc$resTable <- df
df
} else NULL
},digits=4)
shiny::observeEvent(input$downloadtable,
{
write.csv(file=input[["adduct-table"]],x=as.matrix(rv_adduc[["resTable"]]),row.names = F,col.names = names(rv_adduc[["resTable"]]))
})
shiny::observeEvent(input$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$idslider]],linput=res)
})
## shiny::observeEvent(input$yaxis,{
## rv$yaxis <- input$yaxis
## })
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)
}