From 8b1a172ec0170da81d044e577f2bb47c8b9eec4c Mon Sep 17 00:00:00 2001
From: Jessy Krier <jessy.krier@ext.uni.lu>
Date: Mon, 22 Jul 2019 10:41:34 +0200
Subject: [PATCH] Update shiny in R/mix.R
* R/mix.R(presc.shiny): Updated.
---
R/mix.R | 85 ++++++++++++++++++++++++++++++++++-----------------------
1 file changed, 51 insertions(+), 34 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index 9cc4af8..6ccbe5b 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -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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