R/Module_FeatureReportModule.R
In mjhelf/Mosaic: 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/Mosaic documentation built on April 28, 2022, 11:32 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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")
# )
)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.