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Commit 77a4a5f9 authored by Todor Kondic's avatar Todor Kondic
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Add save button 

* R/mix.R: Modified server to test for button clicks.
parent 5589185a
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1 merge request!16ability to screen for mass, not SMILES in NT cases; for preProc's QC
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R/mix.R
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......@@ -520,14 +520,15 @@ mb.p<-function(mb,infodir,fn_stgs,cl=F) {
##' @return Nothing useful.
##' @author Jessy Krier
##' @author Mira Narayanan
presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,prescdf){
modemap=list(pH="MpHp_mass",
mH="MmHm_mass",
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
default_min_rt=0
default_max_rt=40
DEFAULT_RT_RANGE=c(0,40)
default_min_rt=DEFAULT_RT_RANGE[1]
default_max_rt=DEFAULT_RT_RANGE[2]
dfdir <- file.path(wd,"prescreen")
wd1 <- wd[[1]]
......@@ -540,13 +541,35 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
zz <- RChemMass::getSuspectFormulaMass(smile)
zz[[modemap[[mode]]]]
})
for (col in c("MS1","MS2","Alignment","Intensity","AboveNoise","Comments")) {
if (is.null(prescdf[[col]])) prescdf[[col]] <- rep(T,length(prescdf$ID))
}
#message("Masses:",masses)
# return(osmesi)
## Get the basenames of eic files.
eics <- list.files(path=dfdir[[1]],patt=".*eic.csv")
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
tags <- levels(factor(prescdf$tag))
spectProps <- sapply(tags,function (tag) paste("spectProps",tag,sep=""))
idsliderrange <- range(df$ID)
tabPanelList <- lapply(tags, function(tag) {
shiny::tabPanel(tag, shiny::checkboxGroupInput(paste("spectProps",tags,sep=""), "Quality Control",
c("MS1" = T,
"MS2" = T,
"Alignment" = T,
"Intensity" = T,
"AboveNoise" = T)),
shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
shiny::verbatimTextOutput(paste("value",tag,sep="")))})
nvp <- do.call(shiny::navlistPanel, tabPanelList)
ui <- shinydashboard::dashboardPage(
shinydashboard::dashboardHeader(title = "Prescreening"),
shinydashboard::dashboardSidebar(
......@@ -557,45 +580,40 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
shinydashboard::dashboardBody(
shiny::fluidRow(
shinydashboard::box(
title = "MS Prescreening", width = 6, height = "80px", background = "blue", ""
title = "MS Prescreening", width = 7, height = "80px", background = "blue", ""
),
shinydashboard::box(
title = "Compound ID N°",width = 6, height = "80px", background = "olive",
title = "Compound ID N°",width = 5, height = "80px", background = "olive",
shiny::textOutput("compoundID")
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot", width = 6, solidHeader = TRUE, collapsible = TRUE,
shiny::plotOutput("plot1", width = "100%", height = "900px", click = NULL,
dblclick = NULL, hover = NULL, hoverDelay = NULL,
hoverDelayType = NULL, brush = NULL, clickId = NULL,
hoverId = NULL)
title = "Plot", width = 7, solidHeader = TRUE, 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", icon = shiny::icon("save"))
),
shinydashboard::box(
title = "Compounds", solidHeader = TRUE, collapsible = TRUE, "", shiny::br(),
title = "Compounds", width=5,solidHeader = TRUE, collapsible = TRUE, "", shiny::br(),
shiny::sliderInput("idslider", "Compound number:", idsliderrange[1], idsliderrange[2], value=1,step=1)
),
shinydashboard::box(
title = "Plot x axis range", width = 3, solidHeader = TRUE, collapsible = TRUE,
title = "Plot x axis range", width = 5, solidHeader = TRUE, collapsible = TRUE,
shiny::numericInput("min_val", "Minimum x Axis Value", default_min_rt),
shiny::numericInput("max_val", "Maximum x Axis Value", default_max_rt)
),
shinydashboard::box(
title = "Prescreening Results", width = 3, solidHeader = TRUE, collapsible = TRUE,
shiny::checkboxGroupInput("variable", "Checkboxes:",
c("MS1" = "MS1 present",
"MS2" = "MS2 present",
"Alignment" = "Alignment MS1/MS2",
"Intensity" = "Intensity is good",
"Noise" = "MS is noisy")),
shiny::textInput("text", "Comments:"),
shiny::tableOutput("data")
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Chemical structure", width = 6, solidHeader = TRUE, collapsible = TRUE)
shinydashboard::box(
title = "Prescreening analysis", width = 5, solidHeader = TRUE, collapsible = TRUE,
shiny::titlePanel(prescdf$set_name),
shiny::uiOutput("nvp"),
shiny::actionButton("submitQA", "Submit", icon = shiny::icon("save"))
)
)
)
)
......@@ -679,7 +697,7 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
## RChemMass::renderSMILES.rcdk(smiles[[i]],coords=c(x1,y1,x2,y2))
gc()
}
clean_rtrange <- function(rtrange) {
x1 <- rtrange[1]
......@@ -688,25 +706,91 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
if (is.na(x2)) x2 <- default_max_rt
c(x1,x2)
}
}
captureQA <- function() {
QAlist <- list()
list(add=function (entry) QAlist[[length(QAlist)+1]]<<-entry,
get=function() QAlist)
}
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$plot1 <- renderPlot(
{
i=input$idslider
rtrange <- c(input$min_val,input$max_val)
plotall(i,rtrange=clean_rtrange(rtrange))
})
session$onSessionEnded(function() {
stopApp()
})
}
)
output$compoundID <- renderText(
output$value <- renderText(
{
input$caption
})
output$compoundID <- renderText(
{
i=input$idslider
})
})
shiny::observeEvent(input$saveplot,
{
i=input$idslider
message("Save plot button pressed.")
pfn <-input$plotname
if (is.na(pfn)) pfn <- "plotCpdID_%i.pdf"
fn <- sprintf(pfn,i)
rtrange <- c(input$min_val,input$max_val)
pdf(file=fn, width=12, height=8)
plotall(i,rtrange=clean_rtrange(rtrange))
dev.off()
})
shiny::observeEvent(input$saveallplots,
{
i=input$idslider
message("Save plot button pressed.")
pfn <-input$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)
for (i in 1:rv$no_cmpds) {
plotall(i,rtrange=rv$default_range)
message("Compound ID ",i," done.")
}
dev.off()
})
shiny::observeEvent(input$idslider,{
i <- input$idslider
tag <- rv$prescdf$tag[[i]]
})
shiny::observeEvent(input$submitQA,{
})
output$nvp <- shiny::renderUI(
{
nvp
})
session$onSessionEnded(function() {
stopApp()
})
}
shiny::shinyApp(ui = ui, server = server)
......
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