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shinyscreen
shinyscreen
Commit ee2b6852 authored by Jessy Krier's avatar Jessy Krier
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On our way to fully function Shiny ...

parent 883b8fa4
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Showing with 37 additions and 17 deletions
R/mix.R
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...@@ -520,7 +520,7 @@ mb.p<-function(mb,infodir,fn_stgs,cl=F) { ...@@ -520,7 +520,7 @@ mb.p<-function(mb,infodir,fn_stgs,cl=F) {
##' @return Nothing useful. ##' @return Nothing useful.
##' @author Jessy Krier ##' @author Jessy Krier
##' @author Mira Narayanan ##' @author Mira Narayanan
presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_setup){ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,prescdf){
modemap=list(pH="MpHp_mass", modemap=list(pH="MpHp_mass",
mH="MmHm_mass", mH="MmHm_mass",
blahnh4="MpNH4_mass", blahnh4="MpNH4_mass",
...@@ -540,23 +540,35 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s ...@@ -540,23 +540,35 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s
zz <- RChemMass::getSuspectFormulaMass(smile) zz <- RChemMass::getSuspectFormulaMass(smile)
zz[[modemap[[mode]]]] zz[[modemap[[mode]]]]
}) })
for (col in c("MS1","MS2","Alignment","Intensity","AboveNoise","Comments")) {
if (is.null(prescdf[[col]])) prescdf[[col]] <- rep(T,length(prescdf$ID))
}
#message("Masses:",masses) #message("Masses:",masses)
# return(osmesi) # return(osmesi)
## Get the basenames of eic files. ## Get the basenames of eic files.
eics <- list.files(path=dfdir[[1]],patt=".*eic.csv") eics <- list.files(path=dfdir[[1]],patt=".*eic.csv")
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')}) maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
tags <- levels(factor(prescdf$tag))
spectProps <- sapply(tags,function (tag) paste("spectProps",tag,sep=""))
idsliderrange <- range(df$ID) idsliderrange <- range(df$ID)
tabPanelList <- lapply(tag_setup$values, function(tag) { tabPanelList <- lapply(tags, function(tag) {
shiny::tabPanel(tag,shiny::checkboxGroupInput(paste("spectProps",tag,sep=""), "Checkboxes:", shiny::tabPanel(tag, shiny::checkboxGroupInput(paste("spectProps",tags,sep=""), "Quality Control",
c("MS1" = "OK", c("MS1" = T,
"MS2" = "OK", "MS2" = T,
"Alignment" = "OK", "Alignment" = T,
"Intensity" = "OK", "Intensity" = T,
"Noise" = "OK")), "AboveNoise" = T)),
shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."), shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
shiny::verbatimTextOutput(paste("value",tag,sep="")))}) shiny::verbatimTextOutput(paste("value",tag,sep="")))})
nvp <- do.call(shiny::navlistPanel, tabPanelList) nvp <- do.call(shiny::navlistPanel, tabPanelList)
ui <- shinydashboard::dashboardPage( ui <- shinydashboard::dashboardPage(
shinydashboard::dashboardHeader(title = "Prescreening"), shinydashboard::dashboardHeader(title = "Prescreening"),
shinydashboard::dashboardSidebar( shinydashboard::dashboardSidebar(
...@@ -567,16 +579,16 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s ...@@ -567,16 +579,16 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s
shinydashboard::dashboardBody( shinydashboard::dashboardBody(
shiny::fluidRow( shiny::fluidRow(
shinydashboard::box( shinydashboard::box(
title = "MS Prescreening", width = 8, height = "80px", background = "blue", "" title = "MS Prescreening", width = 7, height = "80px", background = "blue", ""
), ),
shinydashboard::box( shinydashboard::box(
title = "Compound ID N°",width = 4, height = "80px", background = "olive", title = "Compound ID N°",width = 5, height = "80px", background = "olive",
shiny::textOutput("compoundID") shiny::textOutput("compoundID")
) )
), ),
shiny::fluidRow( shiny::fluidRow(
shinydashboard::box( shinydashboard::box(
title = "Plot", width = 8, solidHeader = TRUE, collapsible = TRUE, title = "Plot", width = 7, solidHeader = TRUE, collapsible = TRUE,
shiny::plotOutput("plot1", width = "100%", height = "750px", click = NULL, shiny::plotOutput("plot1", width = "100%", height = "750px", click = NULL,
dblclick = NULL, hover = NULL, hoverDelay = NULL, dblclick = NULL, hover = NULL, hoverDelay = NULL,
hoverDelayType = NULL, brush = NULL, clickId = NULL, hoverDelayType = NULL, brush = NULL, clickId = NULL,
...@@ -585,17 +597,17 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s ...@@ -585,17 +597,17 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s
shiny::actionButton("saveplot", "Save", icon = shiny::icon("save")) shiny::actionButton("saveplot", "Save", icon = shiny::icon("save"))
), ),
shinydashboard::box( shinydashboard::box(
title = "Compounds", width=4,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) shiny::sliderInput("idslider", "Compound number:", idsliderrange[1], idsliderrange[2], value=1,step=1)
), ),
shinydashboard::box( shinydashboard::box(
title = "Plot x axis range", width = 4, 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("min_val", "Minimum x Axis Value", default_min_rt),
shiny::numericInput("max_val", "Maximum x Axis Value", default_max_rt) shiny::numericInput("max_val", "Maximum x Axis Value", default_max_rt)
), ),
shinydashboard::box( shinydashboard::box(
title = "Prescreening analysis", width = 4, solidHeader = TRUE, collapsible = TRUE, title = "Prescreening analysis", width = 5, solidHeader = TRUE, collapsible = TRUE,
shiny::titlePanel(tag_setup$name), shiny::titlePanel(prescdf$set_name),
shiny::uiOutput("nvp"), shiny::uiOutput("nvp"),
shiny::actionButton("submitQA", "Submit", icon = shiny::icon("save")) shiny::actionButton("submitQA", "Submit", icon = shiny::icon("save"))
...@@ -700,7 +712,7 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s ...@@ -700,7 +712,7 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s
get=function() QAlist) get=function() QAlist)
} }
server <- function(input, output, session) { server <- function(input, output, session) {
rv <- shiny::reactiveValues(prescList=list()) rv <- shiny::reactiveValues(prescList=list(),prescdf=prescdf,spectProps=spectProps,tags=tags)
output$plot1 <- renderPlot( output$plot1 <- renderPlot(
{ {
i=input$idslider i=input$idslider
...@@ -735,8 +747,16 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s ...@@ -735,8 +747,16 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,tag_s
dev.off() dev.off()
}) })
shiny::observeEvent(input$submitQA,{}) shiny::observeEvent(input$idslider,{
i <- input$idslider
tag <- rv$prescdf$tag[[i]]
})
shiny::observeEvent(input$submitQA,{
})
output$nvp <- shiny::renderUI( output$nvp <- shiny::renderUI(
......
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