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Commit 8b1a172e authored by Jessy Krier's avatar Jessy Krier
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Update shiny in R/mix.R 

* R/mix.R(presc.shiny): Updated.
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R/mix.R
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......@@ -526,6 +526,8 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
default_min_rt=0
default_max_rt=40
dfdir <- file.path(wd,"prescreen")
wd1 <- wd[[1]]
......@@ -555,53 +557,50 @@ 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, background = "blue", ""
title = "MS Prescreening", width = 6, height = "80px", background = "blue", ""
),
shinydashboard::box(
title = "ID N°",width = 6, background = "maroon", ""
title = "Compound ID N°",width = 6, height = "80px", background = "olive",
shiny::textOutput("compoundID")
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot", width = 6, solidHeader = TRUE, collapsible = TRUE,
plotOutput("plot1", width = "100%", height = "400px", click = NULL,
shiny::plotOutput("plot1", width = "100%", height = "900px", click = NULL,
dblclick = NULL, hover = NULL, hoverDelay = NULL,
hoverDelayType = NULL, brush = NULL, clickId = NULL,
hoverId = NULL)
),
shinydashboard::box(
title = "Compounds", solidHeader = TRUE, collapsible = TRUE, "", br(),
sliderInput("idslider", "Compound number:", idsliderrange[1], idsliderrange[2], value=1,step=1)
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot x axis range", width = 6, solidHeader = TRUE, collapsible = TRUE,
shinyUI(pageWithSidebar(
headerPanel(""),
sidebarPanel(
numericInput("min_val", "Minimum x Axis Value", 1),
numericInput("max_val", "Maximum x Axis Value", 100),
uiOutput("slider")),
mainPanel()
))
title = "Compounds", solidHeader = TRUE, collapsible = TRUE, "", shiny::br(),
shiny::sliderInput("idslider", "Compound number:", idsliderrange[1], idsliderrange[2], value=1,step=1)
),
shinydashboard::box(
title = "Prescreening Results", width = 6, solidHeader = TRUE, collapsible = TRUE,
checkboxGroupInput("variable", "Checkboxes:",
c("MS1" = "MS1 present",
"MS2" = "MS2 present",
"Alignment" = "Alignment MS1/MS2",
"Intensity" = "Intensity is good",
"Noise" = "MS is noisy")),
textInput("text", "Comments:"),
tableOutput("data")
)
title = "Plot x axis range", width = 3, 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)
)
)
)
plotall <- function(i) {
plotall <- function(i,rtrange) {
eic <- eics[[i]]
maybekid <- maybekids[[i]]
fn_ini <- lapply(wd,get_stgs_fn)
......@@ -636,9 +635,9 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
rt_rng <- range(sapply(dfs,function(x) x$rt))
rt_rng <- rtrange #range(sapply(dfs,function(x) x$rt))
int_rng <- range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
lgnd <- Map(function(k,v) paste(k,"= ",formatC(v,format="f",digits=rt_digits),sep=''),symbs,rt_max)
layout(matrix(c(1,2,3,3), 2, 2, byrow = TRUE),
......@@ -682,16 +681,34 @@ presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
gc()
}
server <- function(input, output) {
clean_rtrange <- function(rtrange) {
x1 <- rtrange[1]
x2 <- rtrange[2]
if (is.na(x1)) x1 <- default_min_rt
if (is.na(x2)) x2 <- default_max_rt
c(x1,x2)
}
server <- function(input, output, session) {
output$plot1 <- renderPlot(
{
i=input$idslider
plotall(i)
rtrange <- c(input$min_val,input$max_val)
plotall(i,rtrange=clean_rtrange(rtrange))
session$onSessionEnded(function() {
stopApp()
})
}
)
output$compoundID <- renderText(
{
i=input$idslider
})
}
shiny::shinyApp(ui = ui, server = server)
}
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