R/Module_FeatureReportModule.R
In mjhelf/METABOseek: Metaboseek platform
Defines functions
FeatureReportModuleUI
FeatureReportModule
Documented in
FeatureReportModule
FeatureReportModuleUI
#' FeatureReportModule
#'
#' Module for visualization of MS1 and MS2 spectra along with EICs, plus option
#' to plot them together with SIRIUS results in a pdf
#'
#' @inherit MseekModules
#'
#'
#' @param MS2feed temporary solution to feed current MS2 scan in from MS2BrowserModule
#' @param tree feed SIRIUS fragmentation tree in from MS2BrowserModule
#' @param fragments feed SIRIUS fragmentation annotation for the MS2 scan
#'
#' @return
#' Returns its internalValues
#'
#' @describeIn FeatureReportModule server logic
#'
#' @export
FeatureReportModule <- function(input,output, session,
values,
MS2feed = NULL, #TODO: simplify inputs
tree = reactive({}),
fragments = NULL){
ns <- NS(session$ns(NULL))
EICcache <- reactiveValues()
internalValues <- reactiveValues(iSpec1 = reactive({NULL}),
yaxmax = NULL,
reltoCheck = F,
subtitleColumns = "comments")
output$pdfButton <- downloadHandler(filename= function(){
titleout <- "featureReport"
return(paste0(titleout,".pdf"))},
content = function(file){
# if(!is.null(fragments)){
# print(fragments()$fragments)}
grp <- if(!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){values$GlobalOpts$groupBy}else{"grouping"}
featureReport(pdf_settings = list(file = file, width = NULL, height = NULL),
layout_settings = min(values$GlobalOpts$plotCols,length(values$MSData$layouts[[values$MSData$active]][[grp]])),
EICplots = plotEngine(),
MS1 = iSpec1()$plotArgs,
MS2 = MS2spec()$plotArgs,
tree = list(tree = tree(),
resolution = 5000),
fragments = if(!is.null(fragments)){
fragments()
}else{NULL},
selectMS2 = if(is.null(MS2feed()$spec$sel)){NULL}
else{names(values$MSData$data)[basename(names(values$MSData$data)) %in% basename(MS2feed()$spec$sel$File)]}
)
},
contentType = "application/pdf")
output$pdfTree <- downloadHandler(filename= function(){
titleout <- "TreeOnly"
return(paste0(titleout,".pdf"))},
content = function(file){
plotTree(tree = tree(),
resolution = 5000,
filename = file)
},
contentType = "application/pdf")
plotEngine <- reactive({
if(!is.null(values$MSData$data) && !is.null(values$MSData$layouts[[values$MSData$active]]$grouping)){
rtmid <- if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"rt"]}
mzmid <- if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}
RTall <- values$GlobalOpts$RTtoggle
adducts <- if(is.null(values$MSData$massShifts$shifts)){0}else{values$MSData$massShifts$shifts}
RTcorrect <- if(is.null(input$RtCorrActive) || !input$RtCorrActive){NULL}else{values$MSData$RTcorr}
# mzx <- data.frame(mzmin = mzmid - mzmid*values$GlobalOpts$PPMwindow*1e-6,
# mzmax = mzmid + mzmid*values$GlobalOpts$PPMwindow*1e-6)
if(any(RTall, is.null(rtmid))){ # any can handle NULL, seems more flexible than ||
rtmid <- NULL
rtx <- NULL
}else{
rtx <- data.frame(rtmin = rtmid - values$GlobalOpts$RTwindow,
rtmax = rtmid + values$GlobalOpts$RTwindow)
}
#generate mz boundary df
if(any(values$GlobalOpts$TICtoggle, is.null(mzmid)) ){
mzmid <- if(!is.null(rtmid)){rep(100,length(rtmid))}else{100}
mzx <- data.frame(mzmin = mzmid-1,
mzmax = mzmid+1)
}else{
mzx <- data.frame(mzmin = mzmid - mzmid*values$GlobalOpts$PPMwindow*1e-6,
mzmax = mzmid + mzmid*values$GlobalOpts$PPMwindow*1e-6)
}
EICcache[[values$MSData$active]] <- multiEICplus(rawdata= values$MSData$data[basename(names(values$MSData$data)) %in% basename(values$MSData$layouts[[values$MSData$active]]$filelist) ],
mz = mzx,
rt = if(is.null(RTcorrect)){rtx}else{NULL},
rnames = row.names(mzmid), #major item names
byFile = F, #if true, table will be sorted by rawfile, otherwise by feature
adducts,
RTcorr = RTcorrect
)
#make subtitles
subtitles <- NULL
if(length(internalValues$subtitleColumns) > 0 && internalValues$subtitleColumns != ""){
subtitles <- paste0(internalValues$subtitleColumns[1], ": ",
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],internalValues$subtitleColumns[1]])
if(length(internalValues$subtitleColumns) > 1){
for( i in 2:length(internalValues$subtitleColumns)){
subtitles <- paste0(subtitles, " ", internalValues$subtitleColumns[i], ": ",
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],internalValues$subtitleColumns[i]])
}
}
}
if(!is.null(values$GlobalOpts$colorBy)
&& values$GlobalOpts$colorBy %in% c("grouping", "grouping2")
&&!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){
cr <- makeColorscheme(maingroup = values$MSData$layouts[[values$MSData$active]][[values$GlobalOpts$groupBy]],
colorgroup =values$MSData$layouts[[values$MSData$active]][[values$GlobalOpts$colorBy]],
colrange = values$GlobalOpts$colorscheme,
transparency = values$GlobalOpts$plotTransparency)
}else{
cr <- values$GlobalOpts$colorscheme
}
grp <- if(!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){values$GlobalOpts$groupBy}else{"grouping"}
list(rtmid = rtmid,
mzmid = mzmid,
glist = values$MSData$layouts[[values$MSData$active]][[grp]],
cols = min(values$GlobalOpts$plotCols,length(values$MSData$layouts[[values$MSData$active]][[grp]])),
colrange = cr,
transparency = values$GlobalOpts$plotTransparency,
RTall = values$GlobalOpts$RTtoggle,
TICall = values$GlobalOpts$TICtoggle || is.null(values$featureTables$Maintable$selected_rows),
rtw = values$GlobalOpts$RTwindow,
ppm = values$GlobalOpts$PPMwindow,
rdata = values$MSData$data[basename(names(values$MSData$data)) %in% basename(values$MSData$layouts[[values$MSData$active]]$filelist) ],
pdfFile = NULL,
leadingTIC = F,
lw = values$GlobalOpts$plotLw,
adducts = if(is.null(values$MSData$massShifts$shifts)){0}else{values$MSData$massShifts$shifts},
cx = values$GlobalOpts$plotCx,
midline = values$GlobalOpts$MLtoggle,
yzoom = values$GlobalOpts$plotYzoom,
RTcorrect = if(is.null(input$RtCorrActive) || !input$RtCorrActive){NULL}else{values$MSData$RTcorr},
importEIC = EICcache[[values$MSData$active]],
globalYmax = internalValues$reltoCheck,
subtitles = subtitles,
relPlot = values$GlobalOpts$relPlotToggle,
raise = values$GlobalOpts$raiseToggle,
RescaleExclude = "MS2"
)
}else{
NULL
}
})
output$mainPlotEICsPre <- renderPlot({
if(!is.null(plotEngine())){
do.call(EICgeneral, plotEngine())
}
}, bg = "white", execOnResize = T)
mainPlotHeight <- reactive({if(!is.null(values$MSData$active) && values$MSData$active != ""){
sizeFactor <- if(!is.null(input$miniPlots) && input$miniPlots){0.4}else{1}
paste0(sizeFactor*(ceiling(length(values$MSData$layouts[[values$MSData$active]]$grouping)/min(values$GlobalOpts$plotCols,
length(values$MSData$layouts[[values$MSData$active]]$grouping)))*400+100),"px")
}
else{"auto"}
})
output$mainPlotEICs <- renderUI({
if(!is.null(values$MSData$data)){
plotOutput(ns("mainPlotEICsPre"),
height = mainPlotHeight()
)
}
})
observe({if(!is.null(values$MSData$active) && !is.null(EICcache[[values$MSData$active]])) {
maxI <- which.max(EICcache[[values$MSData$active]][[1]][,"intmax"])
maxsc <- which.max(EICcache[[values$MSData$active]][[1]][maxI,"intensity"][[1]])
EICcache$iSpec1_feed <- list(File = row.names(EICcache[[values$MSData$active]][[1]])[maxI],
scan = EICcache[[values$MSData$active]][[1]][maxI,"scan"][[1]][maxsc],
rt = EICcache[[values$MSData$active]][[1]][maxI,"rt"][[1]][maxsc]
)
}else{
EICcache$iSpec1_feed <- NULL
}
})
# iSpec1_feed <- eventReactive(EICcache[[values$MSData$active]],{
#
# if(!is.null(EICcache[[values$MSData$active]])){
# maxI <- which.max(EICcache[[values$MSData$active]][[1]][,"intmax"])
# maxsc <- which.max(EICcache[[values$MSData$active]][[1]][maxI,"intensity"][[1]])
# return(list(File = row.names(EICcache[[values$MSData$active]][[1]])[maxI],
# scan = EICcache[[values$MSData$active]][[1]][maxI,"scan"][[1]][maxsc],
# rt = EICcache[[values$MSData$active]][[1]][maxI,"rt"][[1]][maxsc]
#
# ))
# }
# })
# output$siriusTreePlot <- DiagrammeR::renderGrViz({ if(!is.null(tree) && !is.null(tree()) ){
#
# tree()
#
# } })
iSpec1 <- callModule(Specmodule,"Spec1", tag = ns("Spec1"),
set = reactive({
if(is.null(MS2spec()$plotArgs) || is.null(MS2feed()) || is.null(MS2feed()$spec$sel) || length(MS2feed()$spec$sel$File) <1){
list(spec = list(xrange = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{c(values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]-10,
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]+10)},
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = if(!is.null(EICcache$iSpec1_feed)){list(File = EICcache$iSpec1_feed$File[[1]],
scan = EICcache$iSpec1_feed$scan[[1]],
rt = EICcache$iSpec1_feed$rt[[1]])}else{NULL},
data = NULL,
mz = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data)
}else{
tryCatch({
targets <- MS2feed()$spec$sel
ms1targets <- list(File = targets$File)
ms1targets$scan <- sapply(seq(length(targets$File)),function(n){ which.min(abs(values$MSData$data[[which(basename(names( values$MSData$data)) == targets$File[n])]]@scantime - targets$rt[n]))})
ms1targets$rt <- sapply(seq(length(targets$File)),function(n){values$MSData$data[[which(basename(names( values$MSData$data)) == targets$File[n])]]@scantime[ms1targets$scan[n]]})
list(spec = list(xrange = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{c(values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]-3,
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]+7)},
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = ms1targets,
data = NULL,
mz = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = T, #input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data,
moreArgs = list(k = 10))
},
error = function(e){
print("ERROR occurred")
print(targets)
list(spec = list(xrange = NULL,
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = NULL,
data = NULL,
mz = NULL),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = T, #input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data,
moreArgs = list(k = 10))
})
}
}),
keys = reactive({values$GlobalOpts$keyinput.keydown})#,
# static = list(title = "MS1 spectrum")
)
observeEvent(iSpec1,{internalValues$iSpec1 <- iSpec1},
once = TRUE,
ignoreNULL = FALSE)
MS2spec <- callModule(Specmodule,"ms2spec", tag = ns("ms2spec"),
set = reactive({MS2feed()}),
keys = reactive({values$GlobalOpts$keyinput.keydown})
)
SelectMSGrouping <- callModule(SelectMSGroupingModule, "selectLayout",
values = reactiveValues(MSData = values$MSData),
static = list(editOnly = F)
)
output$reltocheck <- renderUI({
div(title = "Plot EICs for all groups to the same scale (the highest intensity value in all EICs for a feature).",
checkboxInput(ns("reltoCheck"), "Rescale", value = internalValues$reltoCheck)
)
})
output$subtitleSelect <- renderUI({
div(title = "Select columns to use for the plot subtitle. All columns currently selected for the main table can be used.",
selectizeInput(ns("subtitleselect"), "Subtitle content",
selected = internalValues$subtitleColumns,
choices = colnames(values$featureTables$Maintable$liveView),
multiple = TRUE)
)
})
observeEvent(input$subtitleselect,{
internalValues$subtitleColumns <- input$subtitleselect
})
observeEvent(input$reltoCheck,{
internalValues$reltoCheck <- input$reltoCheck
})
return(internalValues)
}
#' @describeIn FeatureReportModule UI elements
#' @export
FeatureReportModuleUI <- function(id){
ns <- NS(id)
fluidPage(
fluidRow(
#tags$head(
# tags$style(type="text/css", "label{ display: table-cell; text-align: center; vertical-align: middle; } .form-group { display: table-row;}")
#),
column(1,
checkboxInput(ns("RtCorrActive"), "RT correction", value = F)
),
column(1,
checkboxInput(ns("ShowSpec"), "Show spectrum", value = F)
),
column(1,
div(title = "Make EIC plots smaller to gain vertical space", checkboxInput(ns("miniPlots"), "small EICs", value = F))
),
column(1,
htmlOutput(ns("reltocheck"))
),
column(2,
htmlOutput(ns("subtitleSelect"))
),
column(1,
downloadButton(ns("pdfButton"), "Save Plot")
),
column(1,
downloadButton(ns("pdfTree"), "Save Tree")
),
column(4,
SelectMSGroupingModuleUI(ns("selectLayout"))
)
),
fluidRow(
#imageOutput("mainPlotPlaceholder"),
htmlOutput(ns("mainPlotEICs"))),
fluidRow(
column(6,
SpecmoduleUI(ns("Spec1"))
),
column(6,
SpecmoduleUI(ns("ms2spec"))
))#,
# fluidRow(
# DiagrammeR::grVizOutput(ns("siriusTreePlot"), width = "100%", height = "500px")
# )
)
}
mjhelf/METABOseek documentation built on April 27, 2022, 5:13 p.m.
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Defines functions FeatureReportModuleUI FeatureReportModule
Documented in FeatureReportModule FeatureReportModuleUI
#' FeatureReportModule
#'
#' Module for visualization of MS1 and MS2 spectra along with EICs, plus option
#' to plot them together with SIRIUS results in a pdf
#'
#' @inherit MseekModules
#'
#'
#' @param MS2feed temporary solution to feed current MS2 scan in from MS2BrowserModule
#' @param tree feed SIRIUS fragmentation tree in from MS2BrowserModule
#' @param fragments feed SIRIUS fragmentation annotation for the MS2 scan
#'
#' @return
#' Returns its internalValues
#'
#' @describeIn FeatureReportModule server logic
#'
#' @export
FeatureReportModule <- function(input,output, session,
values,
MS2feed = NULL, #TODO: simplify inputs
tree = reactive({}),
fragments = NULL){
ns <- NS(session$ns(NULL))
EICcache <- reactiveValues()
internalValues <- reactiveValues(iSpec1 = reactive({NULL}),
yaxmax = NULL,
reltoCheck = F,
subtitleColumns = "comments")
output$pdfButton <- downloadHandler(filename= function(){
titleout <- "featureReport"
return(paste0(titleout,".pdf"))},
content = function(file){
# if(!is.null(fragments)){
# print(fragments()$fragments)}
grp <- if(!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){values$GlobalOpts$groupBy}else{"grouping"}
featureReport(pdf_settings = list(file = file, width = NULL, height = NULL),
layout_settings = min(values$GlobalOpts$plotCols,length(values$MSData$layouts[[values$MSData$active]][[grp]])),
EICplots = plotEngine(),
MS1 = iSpec1()$plotArgs,
MS2 = MS2spec()$plotArgs,
tree = list(tree = tree(),
resolution = 5000),
fragments = if(!is.null(fragments)){
fragments()
}else{NULL},
selectMS2 = if(is.null(MS2feed()$spec$sel)){NULL}
else{names(values$MSData$data)[basename(names(values$MSData$data)) %in% basename(MS2feed()$spec$sel$File)]}
)
},
contentType = "application/pdf")
output$pdfTree <- downloadHandler(filename= function(){
titleout <- "TreeOnly"
return(paste0(titleout,".pdf"))},
content = function(file){
plotTree(tree = tree(),
resolution = 5000,
filename = file)
},
contentType = "application/pdf")
plotEngine <- reactive({
if(!is.null(values$MSData$data) && !is.null(values$MSData$layouts[[values$MSData$active]]$grouping)){
rtmid <- if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"rt"]}
mzmid <- if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}
RTall <- values$GlobalOpts$RTtoggle
adducts <- if(is.null(values$MSData$massShifts$shifts)){0}else{values$MSData$massShifts$shifts}
RTcorrect <- if(is.null(input$RtCorrActive) || !input$RtCorrActive){NULL}else{values$MSData$RTcorr}
# mzx <- data.frame(mzmin = mzmid - mzmid*values$GlobalOpts$PPMwindow*1e-6,
# mzmax = mzmid + mzmid*values$GlobalOpts$PPMwindow*1e-6)
if(any(RTall, is.null(rtmid))){ # any can handle NULL, seems more flexible than ||
rtmid <- NULL
rtx <- NULL
}else{
rtx <- data.frame(rtmin = rtmid - values$GlobalOpts$RTwindow,
rtmax = rtmid + values$GlobalOpts$RTwindow)
}
#generate mz boundary df
if(any(values$GlobalOpts$TICtoggle, is.null(mzmid)) ){
mzmid <- if(!is.null(rtmid)){rep(100,length(rtmid))}else{100}
mzx <- data.frame(mzmin = mzmid-1,
mzmax = mzmid+1)
}else{
mzx <- data.frame(mzmin = mzmid - mzmid*values$GlobalOpts$PPMwindow*1e-6,
mzmax = mzmid + mzmid*values$GlobalOpts$PPMwindow*1e-6)
}
EICcache[[values$MSData$active]] <- multiEICplus(rawdata= values$MSData$data[basename(names(values$MSData$data)) %in% basename(values$MSData$layouts[[values$MSData$active]]$filelist) ],
mz = mzx,
rt = if(is.null(RTcorrect)){rtx}else{NULL},
rnames = row.names(mzmid), #major item names
byFile = F, #if true, table will be sorted by rawfile, otherwise by feature
adducts,
RTcorr = RTcorrect
)
#make subtitles
subtitles <- NULL
if(length(internalValues$subtitleColumns) > 0 && internalValues$subtitleColumns != ""){
subtitles <- paste0(internalValues$subtitleColumns[1], ": ",
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],internalValues$subtitleColumns[1]])
if(length(internalValues$subtitleColumns) > 1){
for( i in 2:length(internalValues$subtitleColumns)){
subtitles <- paste0(subtitles, " ", internalValues$subtitleColumns[i], ": ",
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],internalValues$subtitleColumns[i]])
}
}
}
if(!is.null(values$GlobalOpts$colorBy)
&& values$GlobalOpts$colorBy %in% c("grouping", "grouping2")
&&!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){
cr <- makeColorscheme(maingroup = values$MSData$layouts[[values$MSData$active]][[values$GlobalOpts$groupBy]],
colorgroup =values$MSData$layouts[[values$MSData$active]][[values$GlobalOpts$colorBy]],
colrange = values$GlobalOpts$colorscheme,
transparency = values$GlobalOpts$plotTransparency)
}else{
cr <- values$GlobalOpts$colorscheme
}
grp <- if(!is.null(values$GlobalOpts$groupBy)
&& values$GlobalOpts$groupBy %in% c("grouping", "grouping2")){values$GlobalOpts$groupBy}else{"grouping"}
list(rtmid = rtmid,
mzmid = mzmid,
glist = values$MSData$layouts[[values$MSData$active]][[grp]],
cols = min(values$GlobalOpts$plotCols,length(values$MSData$layouts[[values$MSData$active]][[grp]])),
colrange = cr,
transparency = values$GlobalOpts$plotTransparency,
RTall = values$GlobalOpts$RTtoggle,
TICall = values$GlobalOpts$TICtoggle || is.null(values$featureTables$Maintable$selected_rows),
rtw = values$GlobalOpts$RTwindow,
ppm = values$GlobalOpts$PPMwindow,
rdata = values$MSData$data[basename(names(values$MSData$data)) %in% basename(values$MSData$layouts[[values$MSData$active]]$filelist) ],
pdfFile = NULL,
leadingTIC = F,
lw = values$GlobalOpts$plotLw,
adducts = if(is.null(values$MSData$massShifts$shifts)){0}else{values$MSData$massShifts$shifts},
cx = values$GlobalOpts$plotCx,
midline = values$GlobalOpts$MLtoggle,
yzoom = values$GlobalOpts$plotYzoom,
RTcorrect = if(is.null(input$RtCorrActive) || !input$RtCorrActive){NULL}else{values$MSData$RTcorr},
importEIC = EICcache[[values$MSData$active]],
globalYmax = internalValues$reltoCheck,
subtitles = subtitles,
relPlot = values$GlobalOpts$relPlotToggle,
raise = values$GlobalOpts$raiseToggle,
RescaleExclude = "MS2"
)
}else{
NULL
}
})
output$mainPlotEICsPre <- renderPlot({
if(!is.null(plotEngine())){
do.call(EICgeneral, plotEngine())
}
}, bg = "white", execOnResize = T)
mainPlotHeight <- reactive({if(!is.null(values$MSData$active) && values$MSData$active != ""){
sizeFactor <- if(!is.null(input$miniPlots) && input$miniPlots){0.4}else{1}
paste0(sizeFactor*(ceiling(length(values$MSData$layouts[[values$MSData$active]]$grouping)/min(values$GlobalOpts$plotCols,
length(values$MSData$layouts[[values$MSData$active]]$grouping)))*400+100),"px")
}
else{"auto"}
})
output$mainPlotEICs <- renderUI({
if(!is.null(values$MSData$data)){
plotOutput(ns("mainPlotEICsPre"),
height = mainPlotHeight()
)
}
})
observe({if(!is.null(values$MSData$active) && !is.null(EICcache[[values$MSData$active]])) {
maxI <- which.max(EICcache[[values$MSData$active]][[1]][,"intmax"])
maxsc <- which.max(EICcache[[values$MSData$active]][[1]][maxI,"intensity"][[1]])
EICcache$iSpec1_feed <- list(File = row.names(EICcache[[values$MSData$active]][[1]])[maxI],
scan = EICcache[[values$MSData$active]][[1]][maxI,"scan"][[1]][maxsc],
rt = EICcache[[values$MSData$active]][[1]][maxI,"rt"][[1]][maxsc]
)
}else{
EICcache$iSpec1_feed <- NULL
}
})
# iSpec1_feed <- eventReactive(EICcache[[values$MSData$active]],{
#
# if(!is.null(EICcache[[values$MSData$active]])){
# maxI <- which.max(EICcache[[values$MSData$active]][[1]][,"intmax"])
# maxsc <- which.max(EICcache[[values$MSData$active]][[1]][maxI,"intensity"][[1]])
# return(list(File = row.names(EICcache[[values$MSData$active]][[1]])[maxI],
# scan = EICcache[[values$MSData$active]][[1]][maxI,"scan"][[1]][maxsc],
# rt = EICcache[[values$MSData$active]][[1]][maxI,"rt"][[1]][maxsc]
#
# ))
# }
# })
# output$siriusTreePlot <- DiagrammeR::renderGrViz({ if(!is.null(tree) && !is.null(tree()) ){
#
# tree()
#
# } })
iSpec1 <- callModule(Specmodule,"Spec1", tag = ns("Spec1"),
set = reactive({
if(is.null(MS2spec()$plotArgs) || is.null(MS2feed()) || is.null(MS2feed()$spec$sel) || length(MS2feed()$spec$sel$File) <1){
list(spec = list(xrange = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{c(values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]-10,
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]+10)},
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = if(!is.null(EICcache$iSpec1_feed)){list(File = EICcache$iSpec1_feed$File[[1]],
scan = EICcache$iSpec1_feed$scan[[1]],
rt = EICcache$iSpec1_feed$rt[[1]])}else{NULL},
data = NULL,
mz = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data)
}else{
tryCatch({
targets <- MS2feed()$spec$sel
ms1targets <- list(File = targets$File)
ms1targets$scan <- sapply(seq(length(targets$File)),function(n){ which.min(abs(values$MSData$data[[which(basename(names( values$MSData$data)) == targets$File[n])]]@scantime - targets$rt[n]))})
ms1targets$rt <- sapply(seq(length(targets$File)),function(n){values$MSData$data[[which(basename(names( values$MSData$data)) == targets$File[n])]]@scantime[ms1targets$scan[n]]})
list(spec = list(xrange = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{c(values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]-3,
values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]+7)},
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = ms1targets,
data = NULL,
mz = if(is.null(values$featureTables$Maintable$selected_rows)){NULL}else{values$featureTables$Maintable$liveView[values$featureTables$Maintable$selected_rows[1],"mz"]}),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = T, #input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data,
moreArgs = list(k = 10))
},
error = function(e){
print("ERROR occurred")
print(targets)
list(spec = list(xrange = NULL,
yrange = NULL,
maxxrange = NULL,
maxyrange = NULL,
sel = NULL,
data = NULL,
mz = NULL),
layout = list(lw = 1,
cex = 1.5,
controls = F,
ppm = values$GlobalOpts$PPMwindow,
active = T, #input$ShowSpec,
highlights = NULL,
height = 350),
msdata = values$MSData$data,
moreArgs = list(k = 10))
})
}
}),
keys = reactive({values$GlobalOpts$keyinput.keydown})#,
# static = list(title = "MS1 spectrum")
)
observeEvent(iSpec1,{internalValues$iSpec1 <- iSpec1},
once = TRUE,
ignoreNULL = FALSE)
MS2spec <- callModule(Specmodule,"ms2spec", tag = ns("ms2spec"),
set = reactive({MS2feed()}),
keys = reactive({values$GlobalOpts$keyinput.keydown})
)
SelectMSGrouping <- callModule(SelectMSGroupingModule, "selectLayout",
values = reactiveValues(MSData = values$MSData),
static = list(editOnly = F)
)
output$reltocheck <- renderUI({
div(title = "Plot EICs for all groups to the same scale (the highest intensity value in all EICs for a feature).",
checkboxInput(ns("reltoCheck"), "Rescale", value = internalValues$reltoCheck)
)
})
output$subtitleSelect <- renderUI({
div(title = "Select columns to use for the plot subtitle. All columns currently selected for the main table can be used.",
selectizeInput(ns("subtitleselect"), "Subtitle content",
selected = internalValues$subtitleColumns,
choices = colnames(values$featureTables$Maintable$liveView),
multiple = TRUE)
)
})
observeEvent(input$subtitleselect,{
internalValues$subtitleColumns <- input$subtitleselect
})
observeEvent(input$reltoCheck,{
internalValues$reltoCheck <- input$reltoCheck
})
return(internalValues)
}
#' @describeIn FeatureReportModule UI elements
#' @export
FeatureReportModuleUI <- function(id){
ns <- NS(id)
fluidPage(
fluidRow(
#tags$head(
# tags$style(type="text/css", "label{ display: table-cell; text-align: center; vertical-align: middle; } .form-group { display: table-row;}")
#),
column(1,
checkboxInput(ns("RtCorrActive"), "RT correction", value = F)
),
column(1,
checkboxInput(ns("ShowSpec"), "Show spectrum", value = F)
),
column(1,
div(title = "Make EIC plots smaller to gain vertical space", checkboxInput(ns("miniPlots"), "small EICs", value = F))
),
column(1,
htmlOutput(ns("reltocheck"))
),
column(2,
htmlOutput(ns("subtitleSelect"))
),
column(1,
downloadButton(ns("pdfButton"), "Save Plot")
),
column(1,
downloadButton(ns("pdfTree"), "Save Tree")
),
column(4,
SelectMSGroupingModuleUI(ns("selectLayout"))
)
),
fluidRow(
#imageOutput("mainPlotPlaceholder"),
htmlOutput(ns("mainPlotEICs"))),
fluidRow(
column(6,
SpecmoduleUI(ns("Spec1"))
),
column(6,
SpecmoduleUI(ns("ms2spec"))
))#,
# fluidRow(
# DiagrammeR::grVizOutput(ns("siriusTreePlot"), width = "100%", height = "500px")
# )
)
}
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