From 72bcd56ed7a602fd72c4e4fa3feed9f9891dec0f Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:04:33 +0100 Subject: [PATCH 1/8] Added dependencies, wrote description --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 53fb9f6..15f062b 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,6 +10,7 @@ Depends: shiny, shinyBS, shinyjs, + shinybusy, DT, colourpicker, Matrix, @@ -29,7 +30,7 @@ Suggests: testthat VignetteBuilder: knitr Maintainer: Hendrik Treutler -Description: DiffLogo is an easy-to-use tool for the discovery of regulated metabolite families. +Description: We present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. License: GPL (>= 2) biocViews: Software, Visualization Collate: From de0dfc71ecc223b97470256e077763b625bf77ad Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:05:18 +0100 Subject: [PATCH 2/8] Added global variable ExportMatrixName #52 --- MetFamily/server.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/MetFamily/server.R b/MetFamily/server.R index 9f65ade..fc795f8 100755 --- a/MetFamily/server.R +++ b/MetFamily/server.R @@ -123,6 +123,9 @@ shinyServer( artifactColor <- "red" selectionNone <- "None" + ## Download names + ExportMatrixName <- NULL + ## GUI constants runRightColumnWidthFull <- 12 legendColumnWidthFull <- 2 From 54cd514a5840b664220ab81bc3e065d1147b9ec5 Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:06:12 +0100 Subject: [PATCH 3/8] Changed export button #52 --- MetFamily/ui.R | 2475 ++++++++++++++++++++++++------------------------ 1 file changed, 1243 insertions(+), 1232 deletions(-) diff --git a/MetFamily/ui.R b/MetFamily/ui.R index ef3cfb9..286a375 100755 --- a/MetFamily/ui.R +++ b/MetFamily/ui.R @@ -1,1232 +1,1243 @@ - -library(htmltools) -library(shiny) -library(shinyBS) -library(shinyjs) -library(DT) - -importParameterSetInit <- list( - minimumIntensityOfMaximalMS2peak = 2000, - minimumProportionOfMS2peaks = 0.05, - neutralLossesPrecursorToFragments = TRUE, - neutralLossesFragmentsToFragments = FALSE, - mzDeviationAbsolute_grouping = 0.01, - mzDeviationInPPM_grouping = 10, - showImportParametersAdvanced = FALSE, - doPrecursorDeisotoping = TRUE, - mzDeviationAbsolute_precursorDeisotoping = 0.01, - mzDeviationInPPM_precursorDeisotoping = 10, - maximumRtDifference = 0.05, - doMs2PeakGroupDeisotoping = TRUE, - mzDeviationAbsolute_ms2PeakGroupDeisotoping = 0.01, - mzDeviationInPPM_ms2PeakGroupDeisotoping = 10 -) - -shinyUI( - ui = navbarPage(title = "MetFamily", - ########################################################################################## - ########################################################################################## - ########################################################################################## - ########################################################################################## - ## tab run - tabPanel( - shinyjs::useShinyjs(), - ############################################################################################## - ## enable / disable actionButtons while process is running - singleton(tags$head(HTML( - ' - - ' - ))), - title = "Run", - ############################################################################################## - ############################################################################################## - ############################################################################################## - ## side panel - conditionalPanel( - condition = "output.showSideBar", - column(width = 4, - tabsetPanel( - id = "runTabs", - ############################################################################################## - ############################################################################################## - ## file input - tabPanel( - title = "Input", - wellPanel( - #div(style="display:inline-block",actionButton(inputId = "test", label = "", icon = icon(name = "chevron-up", lib = "font-awesome"))), - #actionButton(inputId = "test", label = NULL, icon = icon(name = "chevron-up", lib = "font-awesome")),#, width = NULL, ...) - #downloadButton('downloadReport2', 'Export analysis report'), - bsTooltip(id = "fileInputSelection", title = "The user is able to load a project file or to import external data", placement = "bottom", trigger = "hover"), - radioButtons(inputId = "fileInputSelection", label = NULL, choices = c("Import data", "Load project", "Example data"), selected = "Load project", inline = FALSE), - shiny::hr(), - conditionalPanel( - condition = 'input.fileInputSelection == "Load project"', - h4("Project file input"), - p("Please choose a project file"), - bsTooltip(id = "matrixFile", title = "Press to choose an input file", placement = "bottom", trigger = "hover"), - fileInput( - multiple = FALSE, - inputId = 'matrixFile', - label = NULL, #label = 'Choose fragment matrix file', - accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') - ), - fluidRow( - column(width = 6, - bsTooltip(id = "loadProjectData", title = "Press to load the selected project file", placement = "bottom", trigger = "hover"), - disabled(actionButton(inputId = "loadProjectData", label = "Load project data", class="btn-success", width = "100%")) - ),##column - column(width = 6 - - )##column - )##row - ), - conditionalPanel( - condition = 'input.fileInputSelection == "Import data"', - bsTooltip(id = "projectName", title = "Please type the name of the project", placement = "bottom", trigger = "hover"), - textInput(inputId = "projectName", label = "Project name", value = paste("MetFamily project (created ", gsub(" ", "_", gsub(":", ".", Sys.time())), ")", sep = "")), - bsTooltip(id = "projectDescription", title = "Please type a description of this project as free text", placement = "bottom", trigger = "hover"), - tags$style(type="text/css", "textarea {width:100%}"), - tags$textarea(id = 'projectDescription', placeholder = 'Comments here', rows = 3, ""), - #textInput(inputId = "projectDescription", label = "Project description", value = "", placeholder = "Comments here"), - fluidRow( - column(width = 6, - div(style="float:left", - h4("Parameters for import") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "showImportParameters", title = "Display parameters for processing during import", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showImportParameters", label = "Show parameters", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showImportParameters", - fileInput( - multiple = FALSE, - inputId = 'importParameterFileInput', - label = 'Apply parameters from import parameter file', - accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') - ), - h5("Spectrum filter"), - fluidRow( - column(width = 6, - bsTooltip(id = "minimumIntensityOfMaximalMS2peak", title = "A MS/MS spectrum is considered iff the MS/MS feature with maximum intensity is greater or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "minimumIntensityOfMaximalMS2peak", label = "Min. spectrum intensity", value = importParameterSetInit$minimumIntensityOfMaximalMS2peak) - ),##column - column(width = 6, - bsTooltip(id = "minimumProportionOfMS2peaks", title = "A MS/MS feature is considered iff the intensity is greater or equal than the maximum intensity times this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "minimumProportionOfMS2peaks", label = "MS/MS peak proportion", value = importParameterSetInit$minimumProportionOfMS2peaks) - )##column - ),##row - h5("Neutral losses"), - fluidRow( - column(width = 6, - bsTooltip(id = "neutralLossesPrecursorToFragments", title = "Include neutral losses relative to the precursor ion, i.e. the m/z difference between the m/z of the precursor ion and the m/z of each fragment ion of the corresponding MS/MS spectrum", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "neutralLossesPrecursorToFragments", label = "Fragment vs. precursor", value = importParameterSetInit$neutralLossesPrecursorToFragments) - ),##column - column(width = 6, - bsTooltip(id = "neutralLossesFragmentsToFragments", title = "Include neutral losses amongst fragment ions, i.e. the m/z difference between the m/z of all pairs of fragment ions within each MS/MS spectrum; this involves the incorporation of potentially nonexistent neutral losses and needs more time for processing", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "neutralLossesFragmentsToFragments", label = "Fragment vs. fragment", value = importParameterSetInit$neutralLossesFragmentsToFragments) - )##column - ),##row - h5("Fragment grouping"), - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_grouping", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_grouping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_grouping) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_grouping", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_grouping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_grouping) - )##column - ),##row - fluidRow( - column(width = 6, - div(style="float:left", - h4("Advanced parameters") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "showImportParametersAdvanced", title = "Display parameters for processing during import", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showImportParametersAdvanced", label = "Show parameters", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showImportParametersAdvanced", - h5("MS\u00B9 feature deisotoping"), - bsTooltip(id = "doPrecursorDeisotoping", title = "If checked, the set of MS\u00B9 features is deisotoped", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "doPrecursorDeisotoping", label = "MS\u00B9 feature deisotoping", value = importParameterSetInit$doPrecursorDeisotoping), - conditionalPanel( - condition = "input.doPrecursorDeisotoping", - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_precursorDeisotoping", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value (analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_precursorDeisotoping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_precursorDeisotoping) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_precursorDeisotoping", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million, analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_precursorDeisotoping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_precursorDeisotoping) - )##column - )##row - ),##conditional - bsTooltip(id = "maximumRtDifference", title = "A MS\u00B9 feature is considered an isotopic peak if the absolute of the retention time difference to the (putative) monoisotopic peak is smaller or equal than this value (in minutes)", placement = "bottom", trigger = "hover"), - textInput(inputId = "maximumRtDifference", label = "Retention time difference", value = importParameterSetInit$maximumRtDifference), - h5("Fragment deisotoping"), - bsTooltip(id = "doMs2PeakGroupDeisotoping", title = "If checked, the set of MS/MS features is deisotoped", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "doMs2PeakGroupDeisotoping", label = "Fragment deisotoping", value = importParameterSetInit$doMs2PeakGroupDeisotoping), - conditionalPanel( - condition = "input.doMs2PeakGroupDeisotoping", - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", title = "_A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_ms2PeakGroupDeisotoping) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_ms2PeakGroupDeisotoping", title = "A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_ms2PeakGroupDeisotoping) - )##column - )##row - )##conditional - ) - ), - h4("Data file input"), - p("Please choose metabolite profile (MS1 intensity, .txt)"), - bsTooltip(id = "ms1DataFile", title = "Press to choose a metabolite profile", placement = "bottom", trigger = "hover"), - fileInput( - multiple = FALSE, - inputId = 'ms1DataFile', - label = NULL, #label = 'Choose fragment matrix file', - accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') - ), - p("Please choose spectral library (MS/MS, .msp)"), - bsTooltip(id = "ms2DataFile", title = "Press to choose a MS/MS library", placement = "bottom", trigger = "hover"), - fileInput( - multiple = FALSE, - inputId = 'ms2DataFile', - label = NULL, #label = 'Choose fragment matrix file', - accept = c('text/plain', 'msp') - ), - fluidRow( - column(width = 6, - bsTooltip(id = "importMs1Ms2Data", title = "Press to import the selected metabolite profile and MS/MS library", placement = "bottom", trigger = "hover"), - disabled(actionButton(inputId = "importMs1Ms2Data", label = "Import MS\u00B9 and MS/MS data", class="btn-success", width = "100%")) - ),##column - column(width = 6, - bsTooltip(id = "importMs2Data", title = "Press to import the selected MS/MS library without a metabolite profile", placement = "bottom", trigger = "hover"), - disabled(actionButton(inputId = "importMs2Data", label = "Import MS/MS data", class="btn-success", width = "100%")) - )##column - )##row - ),## conditional - conditionalPanel( - condition = 'input.fileInputSelection == "Example data"', - h4("Example data input"), - helpText( - "The data set used as showcase in the MetFamily publication referenced in the tab 'About'." - ), - br(), - h4("Download original metabolite profile and MS/MS library"), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadMsData", title = "Download the original metabolite profile used in the MetFamily publication", placement = "bottom", trigger = "hover"), - downloadButton(outputId = "downloadMsData", label = "Download metabolite profile"), - tags$style(type='text/css', "#downloadMsData { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%", - bsTooltip(id = "downloadMsMsData", title = "Download the original MS/MS library used in the MetFamily publication", placement = "bottom", trigger = "hover"), - downloadButton(outputId = "downloadMsMsData", label = "Download MS/MS library"), - tags$style(type='text/css', "#downloadMsMsData { width:100%}") - ) - )##column - ),##row - br(), - h4("Download generated fragment matrix"), - fluidRow( - column(width = 6, style="width:50%", - bsTooltip(id = "downloadFragmentMatrix", title = "Download the fragment matrix generated from the original metabolite profile and MS/MS library used in the MetFamily publication", placement = "bottom", trigger = "hover"), - downloadButton('downloadFragmentMatrix', 'Download fragment matrix'), - tags$style(type='text/css', "#downloadFragmentMatrix { width:100%}") - ), - column(width = 6, style="width:50%" - - ) - ), - br(), - fluidRow( - column(width = 12, - h4("Download showcase protocol"), - bsTooltip(id = "downloadDocShowcaseProtocol", title = "Download the protocol which is the basis of the results of the showcase in the MetFamily publication", placement = "bottom", trigger = "hover"), - downloadButton('downloadDocShowcaseProtocol', 'Download showcase protocol') - ) - ), - br(), - h4("Load example data"), - fluidRow( - column(width = 6, - bsTooltip(id = "loadExampleData", title = "Press to load the example data set", placement = "bottom", trigger = "hover"), - actionButton(inputId = "loadExampleData", label = "Load example data", class="btn-success", width = "100%") - ),##column - column(width = 6 - - )##column - )##row - )## conditional - ),##well - wellPanel( - h4("Input status"), - bsTooltip(id = "fileInfo", title = "The current input status", placement = "bottom", trigger = "hover"), - verbatimTextOutput(outputId = "fileInfo") - )#,## well panel - #uiOutput("errorPopupDialog") - ),## tab panel - ############################################################################################## - ############################################################################################## - ## global MS2 filter - #navbarMenu("Filter", - tabPanel( - title = "MS/MS filter", - conditionalPanel( - condition = "output.showGUI", - wellPanel( - ############################################################################################## - ## MS2 filter - h4("Global MS/MS filter"), - ############################################################################################## - ## MS2 plot - fluidRow( - column(width = 6, - div(style="float:left", - h4("Fragment overview") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "showFragmentPlot", title = "Display m/z and frequency of frequent fragments", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showFragmentPlot", label = "Show frequent fragments", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showFragmentPlot", - plotOutput(height = 200, - outputId = "fragmentPlot", - #hover = "fragmentPlot_hover", - hover = hoverOpts( - id = "fragmentPlot_hover", - delay = 50, - delayType = "debounce" - ), - click = "fragmentPlot_click", - dblclick = "fragmentPlot_dblclick", - #brush = "fragmentPlot_brush" - brush = brushOpts( - id = "fragmentPlot_brush", - resetOnNew = TRUE, - direction = "x", - delay = 00, - delayType = "debounce" - ) - ) - ), - fluidRow( - column(width = 11, - bsTooltip(id = "globalFilter_ms2_masses1", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "globalFilter_ms2_masses1", placeholder = 'E.g. 161.0443', label = "MS/MS spectrum includes m/z(s) #1") - ), - column(width = 1, - h4("or") - ) - ), - fluidRow( - column(width = 11, - bsTooltip(id = "globalFilter_ms2_masses2", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "globalFilter_ms2_masses2", placeholder = 'E.g. -88.01808', label = "MS/MS spectrum includes m/z(s) #2") - ), - column(width = 1, - h4("or") - ) - ), - fluidRow( - column(width = 11, - bsTooltip(id = "globalFilter_ms2_masses3", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "globalFilter_ms2_masses3", placeholder = 'E.g. 96.969, -162.053', label = "MS/MS spectrum includes m/z(s) #3") - ), - column(width = 1, - h4("") - ) - ), - bsTooltip(id = "globalFilter_ms2_ppm", title = "The MS/MS feature matching allows this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "globalFilter_ms2_ppm", placeholder = 'PPM number here', label = "PPM"), - ############################################################################################## - ## filter button - fluidRow( - column(width = 6, - div(style="float:left;width:100%", - bsTooltip(id = "applyGlobalMS2filters", title = "Press to determine the global set of MS\u00B9 features which MS/MS spectra comprise the given MS/MS features", placement = "bottom", trigger = "hover"), - actionButton(inputId = "applyGlobalMS2filters", label = "Apply MS/MS filter", class="btn-success", width = "100%") - ) - ),##column - column(width = 6, - div(style="float:right;width:100%", - bsTooltip(id = "clearGlobalMS2filters", title = "Press to clear the global MS/MS filter", placement = "bottom", trigger = "hover"), - actionButton(inputId = "clearGlobalMS2filters", label = "Clear MS/MS filter", class="btn-danger", width = "100%") - ) - )##column - ),##row - hr(), - h4("Filtered MS\u00B9 features"), - bsTooltip(id = "globalMS2filteredPrecursors", title = "The number of MS\u00B9 features which MS/MS spectra comprise the given MS/MS features", placement = "bottom", trigger = "hover"), - verbatimTextOutput("globalMS2filteredPrecursors"), - conditionalPanel( - condition = "output.globalMS2filterValid", - bsTooltip(id = "downloadGlobalMS2filteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), - downloadButton('downloadGlobalMS2filteredPrecursors', 'Download reduced project file') - ) - )## well - ),## conditional panel - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - ) - )## conditional panel - ),## tab panel - ############################################################################################## - ############################################################################################## - ## sample selection - tabPanel( - title = "Sample filter", - conditionalPanel( - condition = "output.showGUI", - wellPanel( - ############################################################################################## - ## sample table - DT::dataTableOutput("sampleTable"), - bsTooltip(id = "updateSampleTable", title = "Updates the order and the exclusion status of samples", placement = "bottom", trigger = "hover"), - actionButton(inputId = "updateSampleTable", label = "Apply sample order and exclusion status", class="btn-success") - )##well - ),## conditiojal panel - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - )## conditional panel - ),## tab panel - #), - ############################################################################################## - ############################################################################################## - ## PCA - tabPanel( - title = "PCA", - conditionalPanel( - condition = "output.showGUI && output.globalMS2filterValid", - wellPanel( - ############################################################################################## - ## HCA group and abundance filter - fluidRow( - column(width = 7, - div(style="float:left", - h4("MS\u00B9 abundance filter for PCA") - ) - ),##column - column(width = 5, - div(style="float:right", - bsTooltip(id = "showPCAfilterOptions", title = "Display filter settings", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showPCAfilterOptions", label = "Show filter settings", value = TRUE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showPCAfilterOptions", - bsTooltip(id = "pcaFilter_average", title = "The average MS\u00B9 abundance should be greater or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "pcaFilter_average", placeholder = 'E.g. 10000', label = "Average MS\u00B9 abundance"), - bsTooltip(id = "pcaFilter_lfc", title = "The log2-fold change [ log2( mean(group one) / mean(group two) ) ] between the average MS\u00B9 abundances should be greater/smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "pcaFilter_lfc", placeholder = 'E.g. 2 or -2', label = "MS\u00B9 log2-fold change"), - fluidRow(style="overflow-y:scroll; - max-height: 200px;", - column(width = 7, - div(style="float:left; - width:100%;", - tags$div(title="Please select the set of sample groups", - checkboxGroupInput(inputId = "pcaGroups", label = "Groups", choices = c("")) - ) - ) - ),##column - column(width = 5, - fluidRow(style = "vertical-align: top", - bsTooltip(id = "filterByPCAgroupSamples", title = "Display and select samples for PCA analysis", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "filterByPCAgroupSamples", label = "Select samples", value = FALSE) - ), - fluidRow(style = "vertical-align: top", - bsTooltip(id = "selectAllPCAGroups", title = "Select all groups", placement = "bottom", trigger = "hover"), - actionButton(inputId = "selectAllPCAGroups", label = "Select all", width = "100%"), - bsTooltip(id = "selectNoPCAGroups", title = "Deselect all groups", placement = "bottom", trigger = "hover"), - actionButton(inputId = "selectNoPCAGroups", label = "Deselect all", width = "100%"), - bsTooltip(id = "selectInvertedPCAGroups", title = "Invert the group selection", placement = "bottom", trigger = "hover"), - actionButton(inputId = "selectInvertedPCAGroups", label = "Invert", width = "100%") - ) - )##column - ),##row - conditionalPanel( - condition = "input.filterByPCAgroupSamples", - fluidRow(style="overflow-y:scroll; - max-height: 200px;", - column(width = 12, - div(style="float:left; - width:100%;", - tags$div(title="Please select the set of samples", - checkboxGroupInput(inputId = "pcaSamples", label = "Samples", choices = c("")) - ))) - ) - ), - - #tags$div(title="Please select the set of sample groups", - # checkboxGroupInput(inputId = "pcaGroups", label = "Groups", choices = c("")) - #), - - bsTooltip(id = "pcaFilterIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "pcaFilterIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), - ############################################################################################## - ## filter button - fluidRow( - column(width = 6, - div(style="float:left;width:100%", - bsTooltip(id = "applyPcaFilters", title = "Press to determine the set of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), - actionButton(inputId = "applyPcaFilters", label = "Apply filter", class="btn-success", width = "100%") - ) - ),##column - column(width = 6, - div(style="float:right;width:100%", - bsTooltip(id = "clearPcaFilters", title = "Press to clear the MS\u00B9 abundance filter for PCA", placement = "bottom", trigger = "hover"), - actionButton(inputId = "clearPcaFilters", label = "Clear filter", class="btn-danger", width = "100%") - ) - )##column - )##row - ),## conditional panel - hr(), - h4("Filtered MS\u00B9 features"), - bsTooltip(id = "pcaFilteredPrecursors", title = "The number of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), - verbatimTextOutput("pcaFilteredPrecursors"), - conditionalPanel( - condition = "output.pcaFilterValid", - bsTooltip(id = "downloadPcaFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), - downloadButton('downloadPcaFilteredPrecursors', 'Download reduced project file') - )##conditional - ),##well - conditionalPanel( - condition = "output.pcaFilterValid", - wellPanel( - bsTooltip(id = "ms1AnalysisMethod", title = "Please choose the method for the analysis of MS\u00B9 abundances", placement = "bottom", trigger = "hover"), - selectInput(multiple = FALSE, inputId = "ms1AnalysisMethod", label = "Method", selected = "PCA", choices = c( - "PCA (Principal Component Analysis)", - "sPCA (Sparse Principal Component Analysis)", - "PLS-DA (Partial Least Squares Discriminant Analysis)", - "sPLS-DA (Sparse Partial Least Squares Discriminant Analysis)" - ), selectize = FALSE), - ############################################################################################## - ## PCA properties - fluidRow( - column(width = 6, - div(style="float:left", - h4("Method properties") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "showPCAadvancedOptions", title = "Display further settings for the selected method", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showPCAadvancedOptions", label = "Show advanced options", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showPCAadvancedOptions", - bsTooltip(id = "pcaScaling", title = "Adjust the scaling of MS\u00B9 abundances for the selected method", placement = "bottom", trigger = "hover"), - selectInput(multiple = FALSE, inputId = "pcaScaling", label = "Scaling", selected = "Pareto", choices = c( - "None", - "Mean center", - "Autoscaling (unit variance)", - "Pareto" - #"Vector normalization", - ), selectize = FALSE), - bsTooltip(id = "pcaLogTransform", title = "MS\u00B9 abundances for the selected method will be log2 transformed", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "pcaLogTransform", label = "Log2 transformation", value = FALSE), - fluidRow( - column( - width = 6, - tags$div(title="Please select the first component", - selectInput(inputId = "pcaDimensionOne", label = "Component 1", choices = c("1", "2", "3", "4", "5"), selected = "1", selectize = FALSE) - ) - ), - column( - width = 6, - tags$div(title="Please select the second component", - selectInput(inputId = "pcaDimensionTwo", label = "Component 2", choices = c("1", "2", "3", "4", "5"), selected = "2", selectize = FALSE) - ) - ) - ) - ), - fluidRow( - column(width = 6, - bsTooltip(id = "drawPCAplots", title = "Display the scores and the loadings plot given the set of filtered MS\u00B9 features and settings of the selected method", placement = "bottom", trigger = "hover"), - actionButton(inputId = "drawPCAplots", label = "Perform analysis", class="btn-success", width = "100%") - ),##column - column(width = 6 - ## nothing - )##column - )##row - )##well - )## conditiojal panel - ),## conditiojal panel - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - ),## conditional panel - conditionalPanel( - condition = "output.showGUI && !output.globalMS2filterValid", - wellPanel( - h4("Please apply a valid MS/MS filter") - )## well panel - )## conditional panel - ),## tab panel - ############################################################################################## - ############################################################################################## - ## HCA - tabPanel( - title = "HCA", - conditionalPanel( - condition = "output.showGUI && output.globalMS2filterValid", - wellPanel( - ############################################################################################## - ## HCA group and abundance filter - fluidRow( - column(width = 7, - div(style="float:left", - h4("MS\u00B9 abundance filter for HCA") - ) - ),##column - column(width = 5, - div(style="float:right", - bsTooltip(id = "showHCAfilterOptions", title = "Display filter settings", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showHCAfilterOptions", label = "Show filter settings", value = TRUE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showHCAfilterOptions", - bsTooltip(id = "hcaFilter_average", title = "The average MS\u00B9 abundance should be greater or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "hcaFilter_average", placeholder = 'E.g. 10000', label = "Average MS\u00B9 abundance"), - bsTooltip(id = "hcaFilter_lfc", title = "The log2-fold change [ log2( mean(group one) / mean(group two) ) ] between the average MS\u00B9 abundances should be greater/smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "hcaFilter_lfc", placeholder = 'E.g. 2 or -2', label = "MS\u00B9 log2-fold change"), - fluidRow(style = "overflow-y:scroll; - max-height: 200px", - #border: 1px solid #cccccc; - column( - width = 6, - tags$div( - title="Please select the first sample group", - radioButtons(inputId = "hcaFilterGroupOne", label = "Group 1", choices = c("")) - ) - ), - column( - width = 6, - tags$div( - title="Please select the second sample group", - radioButtons(inputId = "hcaFilterGroupTwo", label = "Group 2", choices = c("")) - ) - ) - ), - bsTooltip(id = "hcaFilterIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "hcaFilterIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), - ############################################################################################## - ## filter button - fluidRow( - column(width = 6, - div(style="float:left;width:100%", - bsTooltip(id = "applyHcaFilters", title = "Press to determine the set of MS\u00B9 features which fulfill the given filter criteria", placement = "bottom", trigger = "hover"), - actionButton(inputId = "applyHcaFilters", label = "Apply filter", class="btn-success", width = "100%") - ) - ),##column - column(width = 6, - div(style="float:right;width:100%", - bsTooltip(id = "clearHcaFilters", title = "Press to clear the MS\u00B9 abundance filter for HCA", placement = "bottom", trigger = "hover"), - actionButton(inputId = "clearHcaFilters", label = "Clear filter", class="btn-danger", width = "100%") - ) - )##column - )##row - ),## conditional panel - # ),##well panel - # wellPanel( - hr(), - h4("Filtered MS\u00B9 features"), - bsTooltip(id = "hcaFilteredPrecursors", title = paste("The number of MS\u00B9 features which fulfill the given filter criteria. HCA analysis is only possible for less than", - 5000, #maximumNumberOfPrecursorsForHca, - "MS\u00B9 features."), - placement = "bottom", trigger = "hover"), - verbatimTextOutput("hcaFilteredPrecursors"), - conditionalPanel( - condition = "output.hcaFilterValid", - bsTooltip(id = "downloadHcaFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), - downloadButton('downloadHcaFilteredPrecursors', 'Download reduced project file') - )##conditional - ),##well panel - conditionalPanel( - condition = "output.hcaFilterValid", - wellPanel( - ############################################################################################## - ## HCA properties - fluidRow( - column(width = 6, - div(style="float:left", - h4("HCA properties") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "showHCAadvancedOptions", title = "Display further HCA settings", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "showHCAadvancedOptions", label = "Show advanced options", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.showHCAadvancedOptions", - bsTooltip(id = "hcaDistanceFunction", title = "The distance function used for clustering", placement = "bottom", trigger = "hover"), - selectInput(multiple = FALSE, inputId = "hcaDistanceFunction", label = "Distance function", selected = "Jaccard (intensity-weighted)", choices = c( - "Jaccard", - "Jaccard (intensity-weighted)", - "Jaccard (fragment-count-weighted)", - "NDP (Normalized dot product)" - ), selectize = FALSE) - #bsTooltip(id = "hcaClusterMethod", title = "The method used for clustering", placement = "bottom", trigger = "hover"), - #selectInput(multiple = FALSE, inputId = "hcaClusterMethod", label = "Cluster method", selected = "ward.D", choices = c( - # "single", - # "complete", - # "average", - # "mcquitty", - # "median", - # "centroid", - # "ward.D", - # "ward.D2" - #), selectize = FALSE) - ), - fluidRow( - column(width = 6, - bsTooltip(id = "drawHCAplots", title = "Display the HCA dendrogram given the set of filtered MS\u00B9 features and HCA settings", placement = "bottom", trigger = "hover"), - actionButton(inputId = "drawHCAplots", label = "Draw hierarchical cluster", class="btn-success", width = "100%") - ),##column - column(width = 6 - - )##column - ),##row - conditionalPanel( - condition = "output.showGUI && output.plotHcaShown", - br(), - bsTooltip(id = "downloadDistanceMatrix", title = "Download the distance matrix of the currently displayed hierarchical cluster dendrogram", placement = "bottom", trigger = "hover"), - downloadButton('downloadDistanceMatrix', 'Download distance matrix') - ) - )## well panel - )## conditional panel - ),## conditional panel - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - ),## conditional panel - conditionalPanel( - condition = "output.showGUI && !output.globalMS2filterValid", - wellPanel( - h4("Please apply a valid MS/MS filter") - )## well panel - )## conditional panel - ),## tab panel - ############################################################################################## - ############################################################################################## - ## search - tabPanel( - title = "Search", - conditionalPanel( - condition = "output.showGUI && (output.plotHcaShown || output.plotPcaShown)", - #condition = "output.showGUI", - wellPanel( - h4("Search mode"), - bsTooltip(id = "searchMS1orMS2", title = "Please choose the criterion for selecting MS\u00B9 features", placement = "bottom", trigger = "hover"), - radioButtons(inputId = "searchMS1orMS2", label = NULL, choices = c("MS1 feature m/z", "Fragment m/z")), - hr(), - conditionalPanel( - condition = "input.searchMS1orMS2 == 'MS1 feature m/z'", - fluidRow( - column(width = 6, - bsTooltip(id = "searchMS1mass", title = "The MS\u00B9 feature m/z should be similar to at least one of the given values (separated by \",\")", placement = "bottom", trigger = "hover"), - textInput(inputId = "searchMS1mass", placeholder = 'E.g. 592.1792', label = "MS\u00B9 feature m/z('s)") - ),##column - column(width = 6, - bsTooltip(id = "searchMS1massPpm", title = "The specified MS\u00B9 feature m/z allows this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "searchMS1massPpm", placeholder = 'PPM number here', label = "PPM") - )##column - )##row - ),## conditional panel - conditionalPanel( - condition = "input.searchMS1orMS2 == 'Fragment m/z'", - fluidRow( - column(width = 11, - bsTooltip(id = "search_ms2_masses1", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "search_ms2_masses1", placeholder = 'E.g. 161.0443', label = "MS/MS spectrum includes mass(es) #1") - ), - column(width = 1, - h4("or") - ) - ), - fluidRow( - column(width = 11, - bsTooltip(id = "search_ms2_masses2", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "search_ms2_masses2", placeholder = 'E.g. -88.01808', label = "MS/MS spectrum includes mass(es) #2") - ), - column(width = 1, - h4("or") - ) - ), - fluidRow( - column(width = 11, - bsTooltip(id = "search_ms2_masses3", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), - textInput(inputId = "search_ms2_masses3", placeholder = 'E.g. 96.969, -162.053', label = "MS/MS spectrum includes mass(es) #3") - ), - column(width = 1, - h4("") - ) - ), - bsTooltip(id = "searchMS2massPpm", title = "The specified fragment m/z values allow this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "searchMS2massPpm", placeholder = 'PPM number here', label = "PPM") - ),## conditional panel - bsTooltip(id = "searchIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "searchIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), - fluidRow( - column(width = 6, - div(style="float:left;width:100%", - bsTooltip(id = "applySearch", title = "Press to mark the set of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), - actionButton(inputId = "applySearch", label = "Search", class="btn-success", width = "100%") - ) - ),##column - column(width = 6, - div(style="float:right;width:100%", - bsTooltip(id = "clearSearch", title = "Press to clear the selected set of MS\u00B9 feature hits in HCA and PCA", placement = "bottom", trigger = "hover"), - actionButton(inputId = "clearSearch", label = "Clear search", class="btn-danger", width = "100%") - ) - )##column - ),##row - hr(), - h4("MS\u00B9 feature hits"), - bsTooltip(id = "searchInfo", title = "The number of MS\u00B9 features which fulfill the given filter criteria", placement = "bottom", trigger = "hover"), - verbatimTextOutput("searchInfo"), - conditionalPanel( - condition = "output.searchFilterValid & output.filterSearchActive", - bsTooltip(id = "downloadSearchPrecursors", title = "Download a project file which is reduced to the searched set of MS\u00B9 features", placement = "bottom", trigger = "hover"), - downloadButton('downloadSearchPrecursors', 'Download reduced project file') - )##conditional - )##well - ),## conditional panel - conditionalPanel( - #condition = "!(output.analysisType == 'HCA' || output.analysisType == 'PCA')", - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well - ),## conditional panel - conditionalPanel( - condition = "output.showGUI && !(output.plotHcaShown || output.plotPcaShown)", - wellPanel( - h4("Please perform HCA or PCA prior to search") - )## well - )## conditional panel - ),## tab panel - tabPanel( - title = "Classifiers", - conditionalPanel( - condition = "output.showGUI", - wellPanel( - h4("Classifier selection"), - bsTooltip(id = "classifierCount", title = "The number of available classifiers for the semi-automated metabolite family annotation of MS\u00B9 features", placement = "bottom", trigger = "hover"), - verbatimTextOutput(outputId = "classifierCount"), - DT::dataTableOutput("classifierSelectionTable"), - bsTooltip(id = "doAnnotation", title = "Press to automatically annotate metabolite families to spectra ", placement = "bottom", trigger = "hover"), - disabled(actionButton(inputId = "doAnnotation", label = "Perform scan", class="btn-success", width = "100%")) - ) - ), - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - )## conditional panel - ),## tab panel - tabPanel( - title = "Annotations", - conditionalPanel( - condition = "output.showGUI", - wellPanel( - h4("Metabolite family selection"), - bsTooltip(id = "familyCount2", title = "The number of available metabolite families which were annotated among the MS\u00B9 features", placement = "bottom", trigger = "hover"), - verbatimTextOutput(outputId = "familyCount2"), - DT::dataTableOutput("familySelectionTable"), - conditionalPanel( - condition = "output.metaboliteFamilySelected", - #condition = "length(input$familySelectionTable_rows_selected) == 1", - h4("Metabolite family properties"), - bsTooltip(id = "featureCountForFamily", title = "The number of MS\u00B9 features of the selected metabolite family", placement = "bottom", trigger = "hover"), - verbatimTextOutput(outputId = "featureCountForFamily"), - fluidRow( - column(width = 4, - bsTooltip(id = "selectMetaboliteFamily", title = "Press to select this metabolite family", placement = "bottom", trigger = "hover"), - actionButton(inputId = "selectMetaboliteFamily", label = "Select", class="btn-success", width = "100%") - ),##column - column(width = 4, - bsTooltip(id = "renameMetaboliteFamily", title = "Press to rename this metabolite family annotation", placement = "bottom", trigger = "hover"), - actionButton(inputId = "renameMetaboliteFamily", label = "Rename", class="btn-success", width = "100%") - ),##column - column(width = 4, - bsTooltip(id = "removeMetaboliteFamily", title = "Press to remove this metabolite family annotation", placement = "bottom", trigger = "hover"), - actionButton(inputId = "removeMetaboliteFamily", label = "Remove", class="btn-danger", width = "100%") - )##column - ),##row - conditionalPanel( - condition = "output.classifierLoaded", - bsTooltip(id = "metaboliteFamilyComparisonClass", title = "Please choose the class for comparison", placement = "bottom", trigger = "hover"), - selectInput(multiple = FALSE, inputId = "metaboliteFamilyComparisonClass", label = "Compare to class", selected = "[init]", choices = c("[init]"), selectize = FALSE) - ), - plotOutput(height = 250, - outputId = "fragmentPlot2", - #hover = "fragmentPlot2_hover", - hover = hoverOpts( - id = "fragmentPlot2_hover", - delay = 50, - delayType = "debounce" - ), - click = "fragmentPlot2_click", - dblclick = "fragmentPlot2_dblclick", - #brush = "fragmentPlot2_brush" - brush = brushOpts( - id = "fragmentPlot2_brush", - resetOnNew = TRUE, - direction = "x", - delay = 00, - delayType = "debounce" - ) - ), - DT::dataTableOutput("ms1FeatureTableForAnnotation"), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadMetaboliteFamilyConsensusSpectrum", title = "Download the consensus spectrum for the selected metabolite family", placement = "bottom", trigger = "hover"), - downloadButton(outputId = "downloadMetaboliteFamilyConsensusSpectrum", label = "Download consensus spectrum"), - tags$style(type='text/css', "#downloadMetaboliteFamilyConsensusSpectrum { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%", - bsTooltip(id = "downloadMetaboliteFamilyFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), - downloadButton('downloadMetaboliteFamilyFilteredPrecursors', 'Download reduced project file'), - tags$style(type='text/css', "#downloadMetaboliteFamilyFilteredPrecursors { width:100%}") - ) - )##column - )##row - )##conditional - )##well - ),##conditional - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - )## conditional panel - ),## tab panel - tabPanel( - title = "Project", - conditionalPanel( - condition = "output.showGUI", - wellPanel( - h4("MetFamily project"), - fluidRow( - column(width = 6, div(style="float:left;width:100%", - h5("Project name") - )),##column - column(width = 6, div(style="float:right;width:100%", - bsTooltip(id = "projectName2", title = "The name of the project", placement = "bottom", trigger = "hover"), - textInput(inputId = "projectName2", label = NULL, value = "", width = "100%") - ))##column - ),##row - fluidRow( - column(width = 6, div(style="float:left;width:100%", - h5("Project description") - )),##column - column(width = 6, div(style="float:right;width:100%", - bsTooltip(id = "projectDescription2", title = "Please update the description of this project as free text", placement = "bottom", trigger = "hover"), - tags$style(type="text/css", "projectDescription2 {width:100%}"), - tags$textarea(id = 'projectDescription2', placeholder = 'Comments here', rows = 3, ""), - bsTooltip(id = "updateProjectDescription", title = "Press to update the project description", placement = "bottom", trigger = "hover"), - actionButton(inputId = "updateProjectDescription", label = "Update project description", class="btn-success", width = "100%") - ))##column - ),##row - fluidRow( - column(width = 6, - div(style="float:left", - h4("Data import parameters") - ) - ),##column - column(width = 6, - div(style="float:right", - bsTooltip(id = "displayImportParameters", title = "Display parameters used for the initial data import", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "displayImportParameters", label = "Display import parameters", value = FALSE) - ) - )##column - ),##row - conditionalPanel( - condition = "input.displayImportParameters", - h5("Fragment filter"), - fluidRow( - column(width = 6, - bsTooltip(id = "minimumIntensityOfMaximalMS2peak2", title = "A MS/MS spectrum is considered iff the MS/MS feature with maximum intensity is greater or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "minimumIntensityOfMaximalMS2peak2", label = "Min. spectrum intensity", value = 2000) - ),##column - column(width = 6, - bsTooltip(id = "minimumProportionOfMS2peaks2", title = "A MS/MS feature is considered iff the intensity is greater or equal than the maximum intensity times this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "minimumProportionOfMS2peaks2", label = "MS/MS peak proportion", value = 0.05) - )##column - ),##row - h5("Neutral losses"), - fluidRow( - column(width = 6, - bsTooltip(id = "neutralLossesPrecursorToFragments2", title = "Include neutral losses relative to the precursor ion, i.e. the m/z difference between the m/z of the precursor ion and the m/z of each fragment ion of the corresponding MS/MS spectrum", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "neutralLossesPrecursorToFragments2", label = "Fragment vs. precursor", value = TRUE) - ),##column - column(width = 6, - bsTooltip(id = "neutralLossesFragmentsToFragments2", title = "Include neutral losses amongst fragment ions, i.e. the m/z difference between the m/z values of all pairs of fragment ions within each MS/MS spectrum", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "neutralLossesFragmentsToFragments2", label = "Fragment vs. fragment", value = FALSE) - )##column - ),##row - h5("Fragment grouping"), - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_grouping2", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_grouping2", label = "m/z deviation (abs.)", value = 0.01) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_grouping2", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_grouping2", label = "m/z deviation (PPM)", value = 10) - )##column - ),##row - h4("Advanced parameters"), - h5("MS\u00B9 feature deisotoping"), - bsTooltip(id = "doPrecursorDeisotoping2", title = "If checked, the set of MS\u00B9 features is deisotoped", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "doPrecursorDeisotoping2", label = "MS\u00B9 feature deisotoping done", value = TRUE), - conditionalPanel( - condition = "input.doPrecursorDeisotoping2", - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_precursorDeisotoping2", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value (analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_precursorDeisotoping2", label = "m/z deviation (abs.)", value = 0.01) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_precursorDeisotoping2", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million, analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_precursorDeisotoping2", label = "m/z deviation (PPM)", value = 10) - )##column - )##row - ),##conditional - bsTooltip(id = "maximumRtDifference2", title = "A MS\u00B9 feature is considered an isotopic peak if the absolute of the retention time difference to the (putative) monoisotopic peak is smaller or equal than this value (in minutes)", placement = "bottom", trigger = "hover"), - textInput(inputId = "maximumRtDifference2", label = "Retention time difference", value = 0.02), - h5("Fragment deisotoping"), - bsTooltip(id = "doMs2PeakGroupDeisotoping2", title = "If checked, the set of MS/MS features is deisotoped", placement = "bottom", trigger = "hover"), - checkboxInput(inputId = "doMs2PeakGroupDeisotoping2", label = "Fragment deisotoping done", value = TRUE), - conditionalPanel( - condition = "input.doMs2PeakGroupDeisotoping2", - fluidRow( - column(width = 6, - bsTooltip(id = "mzDeviationAbsolute_ms2PeakGroupDeisotoping2", title = "_A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping2", label = "m/z deviation (abs.)", value = 0.01) - ),##column - column(width = 6, - bsTooltip(id = "mzDeviationInPPM_ms2PeakGroupDeisotoping2", title = "A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), - textInput(inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping2", label = "m/z deviation (PPM)", value = 10) - )##column - )##row - )##conditional - ),##conditional - h4("Export"), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadAllPrecursors", title = "Download the full project file", placement = "bottom", trigger = "hover"), - downloadButton(outputId = "downloadAllPrecursors", label = "Export project"), - tags$style(type='text/css', "#downloadAllPrecursors { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%", - bsTooltip(id = "downloadImportParameterSet", title = "Download a parameter file with the parameters which have been used for the initial data import", placement = "bottom", trigger = "hover"), - downloadButton(outputId = "downloadImportParameterSet", label = "Export import parameter set"), - tags$style(type='text/css', "#downloadImportParameterSet { width:100%}") - ) - )##column - ),##row - br(), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadPcaImage", title = "Download the currently displayed PCA plots as image", placement = "bottom", trigger = "hover"), - downloadButton('downloadPcaImage', 'Export PCA as image'), - tags$style(type='text/css', "#downloadPcaImage { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%", - bsTooltip(id = "downloadPcaImageType", title = "The user is able to download the PCA plot as image of different types: Portable Network Graphics (*.png) file, Scalable Vector Graphics (*.svg) file, Portable Document Format (*.pdf) file", placement = "bottom", trigger = "hover"), - radioButtons(inputId = "downloadPcaImageType", label = NULL, choices = c("png", "svg", "pdf"), selected = "png", inline = TRUE, width = "100%") - ) - )##column - ),##row - br(), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadHcaImage", title = "Download the currently displayed HCA plots as image", placement = "bottom", trigger = "hover"), - downloadButton('downloadHcaImage', 'Export HCA as image'), - tags$style(type='text/css', "#downloadHcaImage { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%", - bsTooltip(id = "downloadHcaImageType", title = "The user is able to download the HCA plot as image of different types: Portable Network Graphics (*.png) file, Scalable Vector Graphics (*.svg) file, Portable Document Format (*.pdf) file", placement = "bottom", trigger = "hover"), - radioButtons(inputId = "downloadHcaImageType", label = NULL, choices = c("png", "svg", "pdf"), selected = "png", inline = TRUE, width = "100%") - ) - )##column - ),##row - br(), - fluidRow( - column(width = 6, style="width:50%", - div(style="float:left;width:100%", - bsTooltip(id = "downloadReport", title = "Download the currently displayed HCA plots and PCA plots as report", placement = "bottom", trigger = "hover"), - downloadButton('downloadReport', 'Export analysis report'), - tags$style(type='text/css', "#downloadReport { width:100%}") - ) - ),##column - column(width = 6, style="width:50%", - div(style="float:right;width:100%" - ## nothing here - ) - )##column - )##row - )##well - ),## conditional panel - conditionalPanel( - condition = "!output.showGUI", - wellPanel( - h4("Please import a data file") - )## well panel - )## conditional panel - )## tab panel - )## tab set panel - )## column - ),##conditional - ############################################################################################## - ############################################################################################## - ############################################################################################## - ## plots - #uiOutput("runRightColumn") - source(file = "app_files/ui_rightColumn.R", local = TRUE)$value - ),## tab - ########################################################################################## - ########################################################################################## - ########################################################################################## - ########################################################################################## - ## tab about - tabPanel( - title = "About", - ############################################################################################## - ## intro - wellPanel( - h4(HTML("MetFamily 1.0")), - fluidRow( - column(width = 9, - helpText( - "The MetFamily web application is designed for the identification of regulated metabolite families. This is possible on the basis of metabolite profiles for a set of MS\u00B9 features as well as one MS/MS spectrum for each MS\u00B9 feature. Group-discriminating MS\u00B9 features are identified using a principal component analysis (PCA) of metabolite profiles and metabolite families are identified using a hierarchical cluster analysis (HCA) of MS/MS spectra. Regulated metabolite families are identified by considering group-discriminating MS\u00B9 features from corporate metabolite families." - ) - ),##column - column(width = 3, - tags$a(imageOutput(outputId = "ipbImage", width = "100%", height = "100%"), href='http://www.ipb-halle.de/en/', target='_blank') - #HTML("") - )##column - )## row - ),## well panel - wellPanel( - h4(HTML("Published in Analytical Chemistry (ACS Publications):")), - br(), - h5(HTML("Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies")), - p(HTML("Hendrik Treutler1, Hiroshi Tsugawa2, Andrea Porzel3, Karin Gorzolka1, Alain Tissier4, Steffen Neumann1, and Gerd Ulrich Balcke4*")), - p(HTML(paste( - "", - "1Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, D-06120 Halle/Saale, Germany", "
", - "2RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan", "
", - "3Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle/Saale, Germany", "
", - "4Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Weinberg 3, D-06120 Halle/Saale, Germany", "
", - "*Corresponding author: Gerd Ulrich Balcke Gerd.Balcke@ipb-halle.de - ", sep="" - ))), - br(), - h5(HTML("Abstract")), - p(HTML("The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS\u00B9 abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application “MetFamily”, which is freely available at http://msbi.ipb-halle.de/MetFamily/. MetFamily provides a dynamic link between the patterns based on MS\u00B9-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS\u00B9 patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR.")), - br(), - h5(HTML("Cite")), - p(HTML(paste( - "Hendrik Treutler, Hiroshi Tsugawa, Andrea Porzel, Karin Gorzolka, Alain Tissier, Steffen Neumann, and Gerd Ulrich U. Balcke.
", - "Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.
", - "Analytical chemistry, 88(16):8082-8090, August 2016.
", - "doi:10.1021/acs.analchem.6b01569", - sep = ""))) - ),## well panel - wellPanel( - h4(HTML("Documentation")), - p(HTML("Please find a user guide for the usage of the MetFamily web application below. ")), - bsTooltip(id = "downloadDocUserGuide", title = "Download the user guide for the MetFamily web application", placement = "bottom", trigger = "hover"), - downloadButton('downloadDocUserGuide', 'Download user guide'), - p(HTML("We provide a specification of the input file format. In the MetFamily publication we demonstrated the usage of MetFamily with UPLC-(-)ESI-SWATH-MS/MS data preprocessed with MS-DIAL. In the input specification, however, we demonstrate the generation of these files with GC-EI-MS data processed with xcms and CAMERA We also analyzed idMSMS spectra and LC-MS/MS spectra from DDA in MetFamily.")), - bsTooltip(id = "downloadDocInputSpecification", title = "Download the input specification of the MetFamily web application", placement = "bottom", trigger = "hover"), - downloadButton('downloadDocInputSpecification', 'Download input specification') - ),## well panel - wellPanel( - h4(HTML("Feedback")), - p(HTML("The MetFamily web application is designed to support researchers in the interpretation of comparative metabolomics studies at the level of metabolite families. Please help to improve this tool by comments, bug reports, and feature requests. You can contact Dr. Gerd Balcke via EMail and issues on GitHub.")) - ),## well panel - wellPanel( - h4(HTML("Session info")), - verbatimTextOutput(outputId = "rInfo") - )## well panel - )## tab - )## navBar -)## shinyUI + +library(htmltools) +library(shiny) +library(shinyBS) +library(shinyjs) +library(DT) + +importParameterSetInit <- list( + minimumIntensityOfMaximalMS2peak = 2000, + minimumProportionOfMS2peaks = 0.05, + neutralLossesPrecursorToFragments = TRUE, + neutralLossesFragmentsToFragments = FALSE, + mzDeviationAbsolute_grouping = 0.01, + mzDeviationInPPM_grouping = 10, + showImportParametersAdvanced = FALSE, + doPrecursorDeisotoping = TRUE, + mzDeviationAbsolute_precursorDeisotoping = 0.01, + mzDeviationInPPM_precursorDeisotoping = 10, + maximumRtDifference = 0.05, + doMs2PeakGroupDeisotoping = TRUE, + mzDeviationAbsolute_ms2PeakGroupDeisotoping = 0.01, + mzDeviationInPPM_ms2PeakGroupDeisotoping = 10 +) + +shinyUI( + ui = navbarPage(title = "MetFamily", + + ########################################################################################## + ########################################################################################## + ########################################################################################## + ########################################################################################## + ## tab run + tabPanel( + shinyjs::useShinyjs(), + ############################################################################################## + ## enable / disable actionButtons while process is running + singleton(tags$head(HTML( + ' + + + ' + ))), + singleton(tags$head(tags$style( + HTML(".shiny-notification { + position:fixed; + top: calc(40%); + left: calc(50%); + } + " + )))), + + title = "Run", + ############################################################################################## + ############################################################################################## + ############################################################################################## + ## side panel + conditionalPanel( + condition = "output.showSideBar", + column(width = 4, + tabsetPanel( + id = "runTabs", + ############################################################################################## + ############################################################################################## + ## file input + tabPanel( + title = "Input", + wellPanel( + #div(style="display:inline-block",actionButton(inputId = "test", label = "", icon = icon(name = "chevron-up", lib = "font-awesome"))), + #actionButton(inputId = "test", label = NULL, icon = icon(name = "chevron-up", lib = "font-awesome")),#, width = NULL, ...) + #downloadButton('downloadReport2', 'Export analysis report'), + bsTooltip(id = "fileInputSelection", title = "The user is able to load a project file or to import external data", placement = "bottom", trigger = "hover"), + radioButtons(inputId = "fileInputSelection", label = NULL, choices = c("Import data", "Load project", "Example data"), selected = "Load project", inline = FALSE), + shiny::hr(), + conditionalPanel( + condition = 'input.fileInputSelection == "Load project"', + h4("Project file input"), + p("Please choose a project file"), + bsTooltip(id = "matrixFile", title = "Press to choose an input file", placement = "bottom", trigger = "hover"), + fileInput( + multiple = FALSE, + inputId = 'matrixFile', + label = NULL, #label = 'Choose fragment matrix file', + accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') + ), + fluidRow( + column(width = 6, + bsTooltip(id = "loadProjectData", title = "Press to load the selected project file", placement = "bottom", trigger = "hover"), + disabled(actionButton(inputId = "loadProjectData", label = "Load project data", class="btn-success", width = "100%")) + ),##column + column(width = 6 + + )##column + )##row + ), + conditionalPanel( + condition = 'input.fileInputSelection == "Import data"', + bsTooltip(id = "projectName", title = "Please type the name of the project", placement = "bottom", trigger = "hover"), + textInput(inputId = "projectName", label = "Project name", value = paste("MetFamily project (created ", gsub(" ", "_", gsub(":", ".", Sys.time())), ")", sep = "")), + bsTooltip(id = "projectDescription", title = "Please type a description of this project as free text", placement = "bottom", trigger = "hover"), + tags$style(type="text/css", "textarea {width:100%}"), + tags$textarea(id = 'projectDescription', placeholder = 'Comments here', rows = 3, ""), + #textInput(inputId = "projectDescription", label = "Project description", value = "", placeholder = "Comments here"), + fluidRow( + column(width = 6, + div(style="float:left", + h4("Parameters for import") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "showImportParameters", title = "Display parameters for processing during import", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showImportParameters", label = "Show parameters", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showImportParameters", + fileInput( + multiple = FALSE, + inputId = 'importParameterFileInput', + label = 'Apply parameters from import parameter file', + accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') + ), + h5("Spectrum filter"), + fluidRow( + column(width = 6, + bsTooltip(id = "minimumIntensityOfMaximalMS2peak", title = "A MS/MS spectrum is considered iff the MS/MS feature with maximum intensity is greater or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "minimumIntensityOfMaximalMS2peak", label = "Min. spectrum intensity", value = importParameterSetInit$minimumIntensityOfMaximalMS2peak) + ),##column + column(width = 6, + bsTooltip(id = "minimumProportionOfMS2peaks", title = "A MS/MS feature is considered iff the intensity is greater or equal than the maximum intensity times this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "minimumProportionOfMS2peaks", label = "MS/MS peak proportion", value = importParameterSetInit$minimumProportionOfMS2peaks) + )##column + ),##row + h5("Neutral losses"), + fluidRow( + column(width = 6, + bsTooltip(id = "neutralLossesPrecursorToFragments", title = "Include neutral losses relative to the precursor ion, i.e. the m/z difference between the m/z of the precursor ion and the m/z of each fragment ion of the corresponding MS/MS spectrum", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "neutralLossesPrecursorToFragments", label = "Fragment vs. precursor", value = importParameterSetInit$neutralLossesPrecursorToFragments) + ),##column + column(width = 6, + bsTooltip(id = "neutralLossesFragmentsToFragments", title = "Include neutral losses amongst fragment ions, i.e. the m/z difference between the m/z of all pairs of fragment ions within each MS/MS spectrum; this involves the incorporation of potentially nonexistent neutral losses and needs more time for processing", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "neutralLossesFragmentsToFragments", label = "Fragment vs. fragment", value = importParameterSetInit$neutralLossesFragmentsToFragments) + )##column + ),##row + h5("Fragment grouping"), + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_grouping", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_grouping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_grouping) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_grouping", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_grouping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_grouping) + )##column + ),##row + fluidRow( + column(width = 6, + div(style="float:left", + h4("Advanced parameters") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "showImportParametersAdvanced", title = "Display parameters for processing during import", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showImportParametersAdvanced", label = "Show parameters", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showImportParametersAdvanced", + h5("MS\u00B9 feature deisotoping"), + bsTooltip(id = "doPrecursorDeisotoping", title = "If checked, the set of MS\u00B9 features is deisotoped", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "doPrecursorDeisotoping", label = "MS\u00B9 feature deisotoping", value = importParameterSetInit$doPrecursorDeisotoping), + conditionalPanel( + condition = "input.doPrecursorDeisotoping", + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_precursorDeisotoping", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value (analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_precursorDeisotoping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_precursorDeisotoping) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_precursorDeisotoping", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million, analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_precursorDeisotoping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_precursorDeisotoping) + )##column + )##row + ),##conditional + bsTooltip(id = "maximumRtDifference", title = "A MS\u00B9 feature is considered an isotopic peak if the absolute of the retention time difference to the (putative) monoisotopic peak is smaller or equal than this value (in minutes)", placement = "bottom", trigger = "hover"), + textInput(inputId = "maximumRtDifference", label = "Retention time difference", value = importParameterSetInit$maximumRtDifference), + h5("Fragment deisotoping"), + bsTooltip(id = "doMs2PeakGroupDeisotoping", title = "If checked, the set of MS/MS features is deisotoped", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "doMs2PeakGroupDeisotoping", label = "Fragment deisotoping", value = importParameterSetInit$doMs2PeakGroupDeisotoping), + conditionalPanel( + condition = "input.doMs2PeakGroupDeisotoping", + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", title = "_A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", label = "m/z deviation (abs.)", value = importParameterSetInit$mzDeviationAbsolute_ms2PeakGroupDeisotoping) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_ms2PeakGroupDeisotoping", title = "A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping", label = "m/z deviation (PPM)", value = importParameterSetInit$mzDeviationInPPM_ms2PeakGroupDeisotoping) + )##column + )##row + )##conditional + ) + ), + h4("Data file input"), + p("Please choose metabolite profile (MS1 intensity, .txt)"), + bsTooltip(id = "ms1DataFile", title = "Press to choose a metabolite profile", placement = "bottom", trigger = "hover"), + fileInput( + multiple = FALSE, + inputId = 'ms1DataFile', + label = NULL, #label = 'Choose fragment matrix file', + accept = c('text/comma-separated-values', 'text/plain', 'text/tab-separated-values') + ), + p("Please choose spectral library (MS/MS, .msp)"), + bsTooltip(id = "ms2DataFile", title = "Press to choose a MS/MS library", placement = "bottom", trigger = "hover"), + fileInput( + multiple = FALSE, + inputId = 'ms2DataFile', + label = NULL, #label = 'Choose fragment matrix file', + accept = c('text/plain', 'msp') + ), + fluidRow( + column(width = 6, + bsTooltip(id = "importMs1Ms2Data", title = "Press to import the selected metabolite profile and MS/MS library", placement = "bottom", trigger = "hover"), + disabled(actionButton(inputId = "importMs1Ms2Data", label = "Import MS\u00B9 and MS/MS data", class="btn-success", width = "100%")) + ),##column + column(width = 6, + bsTooltip(id = "importMs2Data", title = "Press to import the selected MS/MS library without a metabolite profile", placement = "bottom", trigger = "hover"), + disabled(actionButton(inputId = "importMs2Data", label = "Import MS/MS data", class="btn-success", width = "100%")) + )##column + )##row + ),## conditional + conditionalPanel( + condition = 'input.fileInputSelection == "Example data"', + h4("Example data input"), + helpText( + "The data set used as showcase in the MetFamily publication referenced in the tab 'About'." + ), + br(), + h4("Download original metabolite profile and MS/MS library"), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "downloadMsData", title = "Download the original metabolite profile used in the MetFamily publication", placement = "bottom", trigger = "hover"), + downloadButton(outputId = "downloadMsData", label = "Download metabolite profile"), + tags$style(type='text/css', "#downloadMsData { width:100%}") + ) + ),##column + column(width = 6, style="width:50%", + div(style="float:right;width:100%", + bsTooltip(id = "downloadMsMsData", title = "Download the original MS/MS library used in the MetFamily publication", placement = "bottom", trigger = "hover"), + downloadButton(outputId = "downloadMsMsData", label = "Download MS/MS library"), + tags$style(type='text/css', "#downloadMsMsData { width:100%}") + ) + )##column + ),##row + br(), + h4("Download generated fragment matrix"), + fluidRow( + column(width = 6, style="width:50%", + bsTooltip(id = "downloadFragmentMatrix", title = "Download the fragment matrix generated from the original metabolite profile and MS/MS library used in the MetFamily publication", placement = "bottom", trigger = "hover"), + downloadButton('downloadFragmentMatrix', 'Download fragment matrix'), + tags$style(type='text/css', "#downloadFragmentMatrix { width:100%}") + ), + column(width = 6, style="width:50%" + + ) + ), + br(), + fluidRow( + column(width = 12, + h4("Download showcase protocol"), + bsTooltip(id = "downloadDocShowcaseProtocol", title = "Download the protocol which is the basis of the results of the showcase in the MetFamily publication", placement = "bottom", trigger = "hover"), + downloadButton('downloadDocShowcaseProtocol', 'Download showcase protocol') + ) + ), + br(), + h4("Load example data"), + fluidRow( + column(width = 6, + bsTooltip(id = "loadExampleData", title = "Press to load the example data set", placement = "bottom", trigger = "hover"), + actionButton(inputId = "loadExampleData", label = "Load example data", class="btn-success", width = "100%") + ),##column + column(width = 6 + + )##column + )##row + )## conditional + ),##well + wellPanel( + h4("Input status"), + bsTooltip(id = "fileInfo", title = "The current input status", placement = "bottom", trigger = "hover"), + verbatimTextOutput(outputId = "fileInfo") + )#,## well panel + #uiOutput("errorPopupDialog") + ),## tab panel + ############################################################################################## + ############################################################################################## + ## global MS2 filter + #navbarMenu("Filter", + tabPanel( + title = "MS/MS filter", + conditionalPanel( + condition = "output.showGUI", + wellPanel( + ############################################################################################## + ## MS2 filter + h4("Global MS/MS filter"), + ############################################################################################## + ## MS2 plot + fluidRow( + column(width = 6, + div(style="float:left", + h4("Fragment overview") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "showFragmentPlot", title = "Display m/z and frequency of frequent fragments", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showFragmentPlot", label = "Show frequent fragments", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showFragmentPlot", + plotOutput(height = 200, + outputId = "fragmentPlot", + #hover = "fragmentPlot_hover", + hover = hoverOpts( + id = "fragmentPlot_hover", + delay = 50, + delayType = "debounce" + ), + click = "fragmentPlot_click", + dblclick = "fragmentPlot_dblclick", + #brush = "fragmentPlot_brush" + brush = brushOpts( + id = "fragmentPlot_brush", + resetOnNew = TRUE, + direction = "x", + delay = 00, + delayType = "debounce" + ) + ) + ), + fluidRow( + column(width = 11, + bsTooltip(id = "globalFilter_ms2_masses1", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "globalFilter_ms2_masses1", placeholder = 'E.g. 161.0443', label = "MS/MS spectrum includes m/z(s) #1") + ), + column(width = 1, + h4("or") + ) + ), + fluidRow( + column(width = 11, + bsTooltip(id = "globalFilter_ms2_masses2", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "globalFilter_ms2_masses2", placeholder = 'E.g. -88.01808', label = "MS/MS spectrum includes m/z(s) #2") + ), + column(width = 1, + h4("or") + ) + ), + fluidRow( + column(width = 11, + bsTooltip(id = "globalFilter_ms2_masses3", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "globalFilter_ms2_masses3", placeholder = 'E.g. 96.969, -162.053', label = "MS/MS spectrum includes m/z(s) #3") + ), + column(width = 1, + h4("") + ) + ), + bsTooltip(id = "globalFilter_ms2_ppm", title = "The MS/MS feature matching allows this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "globalFilter_ms2_ppm", placeholder = 'PPM number here', label = "PPM"), + ############################################################################################## + ## filter button + fluidRow( + column(width = 6, + div(style="float:left;width:100%", + bsTooltip(id = "applyGlobalMS2filters", title = "Press to determine the global set of MS\u00B9 features which MS/MS spectra comprise the given MS/MS features", placement = "bottom", trigger = "hover"), + actionButton(inputId = "applyGlobalMS2filters", label = "Apply MS/MS filter", class="btn-success", width = "100%") + ) + ),##column + column(width = 6, + div(style="float:right;width:100%", + bsTooltip(id = "clearGlobalMS2filters", title = "Press to clear the global MS/MS filter", placement = "bottom", trigger = "hover"), + actionButton(inputId = "clearGlobalMS2filters", label = "Clear MS/MS filter", class="btn-danger", width = "100%") + ) + )##column + ),##row + hr(), + h4("Filtered MS\u00B9 features"), + bsTooltip(id = "globalMS2filteredPrecursors", title = "The number of MS\u00B9 features which MS/MS spectra comprise the given MS/MS features", placement = "bottom", trigger = "hover"), + verbatimTextOutput("globalMS2filteredPrecursors"), + conditionalPanel( + condition = "output.globalMS2filterValid", + bsTooltip(id = "downloadGlobalMS2filteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), + downloadButton('downloadGlobalMS2filteredPrecursors', 'Download reduced project file') + ) + )## well + ),## conditional panel + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + ) + )## conditional panel + ),## tab panel + ############################################################################################## + ############################################################################################## + ## sample selection + tabPanel( + title = "Sample filter", + conditionalPanel( + condition = "output.showGUI", + wellPanel( + ############################################################################################## + ## sample table + DT::dataTableOutput("sampleTable"), + bsTooltip(id = "updateSampleTable", title = "Updates the order and the exclusion status of samples", placement = "bottom", trigger = "hover"), + actionButton(inputId = "updateSampleTable", label = "Apply sample order and exclusion status", class="btn-success") + )##well + ),## conditiojal panel + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + )## conditional panel + ),## tab panel + #), + ############################################################################################## + ############################################################################################## + ## PCA + tabPanel( + title = "PCA", + conditionalPanel( + condition = "output.showGUI && output.globalMS2filterValid", + wellPanel( + ############################################################################################## + ## HCA group and abundance filter + fluidRow( + column(width = 7, + div(style="float:left", + h4("MS\u00B9 abundance filter for PCA") + ) + ),##column + column(width = 5, + div(style="float:right", + bsTooltip(id = "showPCAfilterOptions", title = "Display filter settings", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showPCAfilterOptions", label = "Show filter settings", value = TRUE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showPCAfilterOptions", + bsTooltip(id = "pcaFilter_average", title = "The average MS\u00B9 abundance should be greater or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "pcaFilter_average", placeholder = 'E.g. 10000', label = "Average MS\u00B9 abundance"), + bsTooltip(id = "pcaFilter_lfc", title = "The log2-fold change [ log2( mean(group one) / mean(group two) ) ] between the average MS\u00B9 abundances should be greater/smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "pcaFilter_lfc", placeholder = 'E.g. 2 or -2', label = "MS\u00B9 log2-fold change"), + fluidRow(style="overflow-y:scroll; + max-height: 200px;", + column(width = 7, + div(style="float:left; + width:100%;", + tags$div(title="Please select the set of sample groups", + checkboxGroupInput(inputId = "pcaGroups", label = "Groups", choices = c("")) + ) + ) + ),##column + column(width = 5, + fluidRow(style = "vertical-align: top", + bsTooltip(id = "filterByPCAgroupSamples", title = "Display and select samples for PCA analysis", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "filterByPCAgroupSamples", label = "Select samples", value = FALSE) + ), + fluidRow(style = "vertical-align: top", + bsTooltip(id = "selectAllPCAGroups", title = "Select all groups", placement = "bottom", trigger = "hover"), + actionButton(inputId = "selectAllPCAGroups", label = "Select all", width = "100%"), + bsTooltip(id = "selectNoPCAGroups", title = "Deselect all groups", placement = "bottom", trigger = "hover"), + actionButton(inputId = "selectNoPCAGroups", label = "Deselect all", width = "100%"), + bsTooltip(id = "selectInvertedPCAGroups", title = "Invert the group selection", placement = "bottom", trigger = "hover"), + actionButton(inputId = "selectInvertedPCAGroups", label = "Invert", width = "100%") + ) + )##column + ),##row + conditionalPanel( + condition = "input.filterByPCAgroupSamples", + fluidRow(style="overflow-y:scroll; + max-height: 200px;", + column(width = 12, + div(style="float:left; + width:100%;", + tags$div(title="Please select the set of samples", + checkboxGroupInput(inputId = "pcaSamples", label = "Samples", choices = c("")) + ))) + ) + ), + + #tags$div(title="Please select the set of sample groups", + # checkboxGroupInput(inputId = "pcaGroups", label = "Groups", choices = c("")) + #), + + bsTooltip(id = "pcaFilterIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "pcaFilterIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), + ############################################################################################## + ## filter button + fluidRow( + column(width = 6, + div(style="float:left;width:100%", + bsTooltip(id = "applyPcaFilters", title = "Press to determine the set of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), + actionButton(inputId = "applyPcaFilters", label = "Apply filter", class="btn-success", width = "100%") + ) + ),##column + column(width = 6, + div(style="float:right;width:100%", + bsTooltip(id = "clearPcaFilters", title = "Press to clear the MS\u00B9 abundance filter for PCA", placement = "bottom", trigger = "hover"), + actionButton(inputId = "clearPcaFilters", label = "Clear filter", class="btn-danger", width = "100%") + ) + )##column + )##row + ),## conditional panel + hr(), + h4("Filtered MS\u00B9 features"), + bsTooltip(id = "pcaFilteredPrecursors", title = "The number of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), + verbatimTextOutput("pcaFilteredPrecursors"), + conditionalPanel( + condition = "output.pcaFilterValid", + bsTooltip(id = "downloadPcaFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), + downloadButton('downloadPcaFilteredPrecursors', 'Download reduced project file') + )##conditional + ),##well + conditionalPanel( + condition = "output.pcaFilterValid", + wellPanel( + bsTooltip(id = "ms1AnalysisMethod", title = "Please choose the method for the analysis of MS\u00B9 abundances", placement = "bottom", trigger = "hover"), + selectInput(multiple = FALSE, inputId = "ms1AnalysisMethod", label = "Method", selected = "PCA", choices = c( + "PCA (Principal Component Analysis)", + "sPCA (Sparse Principal Component Analysis)", + "PLS-DA (Partial Least Squares Discriminant Analysis)", + "sPLS-DA (Sparse Partial Least Squares Discriminant Analysis)" + ), selectize = FALSE), + ############################################################################################## + ## PCA properties + fluidRow( + column(width = 6, + div(style="float:left", + h4("Method properties") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "showPCAadvancedOptions", title = "Display further settings for the selected method", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showPCAadvancedOptions", label = "Show advanced options", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showPCAadvancedOptions", + bsTooltip(id = "pcaScaling", title = "Adjust the scaling of MS\u00B9 abundances for the selected method", placement = "bottom", trigger = "hover"), + selectInput(multiple = FALSE, inputId = "pcaScaling", label = "Scaling", selected = "Pareto", choices = c( + "None", + "Mean center", + "Autoscaling (unit variance)", + "Pareto" + #"Vector normalization", + ), selectize = FALSE), + bsTooltip(id = "pcaLogTransform", title = "MS\u00B9 abundances for the selected method will be log2 transformed", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "pcaLogTransform", label = "Log2 transformation", value = FALSE), + fluidRow( + column( + width = 6, + tags$div(title="Please select the first component", + selectInput(inputId = "pcaDimensionOne", label = "Component 1", choices = c("1", "2", "3", "4", "5"), selected = "1", selectize = FALSE) + ) + ), + column( + width = 6, + tags$div(title="Please select the second component", + selectInput(inputId = "pcaDimensionTwo", label = "Component 2", choices = c("1", "2", "3", "4", "5"), selected = "2", selectize = FALSE) + ) + ) + ) + ), + fluidRow( + column(width = 6, + bsTooltip(id = "drawPCAplots", title = "Display the scores and the loadings plot given the set of filtered MS\u00B9 features and settings of the selected method", placement = "bottom", trigger = "hover"), + actionButton(inputId = "drawPCAplots", label = "Perform analysis", class="btn-success", width = "100%") + ),##column + column(width = 6 + ## nothing + )##column + )##row + )##well + )## conditiojal panel + ),## conditiojal panel + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + ),## conditional panel + conditionalPanel( + condition = "output.showGUI && !output.globalMS2filterValid", + wellPanel( + h4("Please apply a valid MS/MS filter") + )## well panel + )## conditional panel + ),## tab panel + ############################################################################################## + ############################################################################################## + ## HCA + tabPanel( + title = "HCA", + conditionalPanel( + condition = "output.showGUI && output.globalMS2filterValid", + wellPanel( + ############################################################################################## + ## HCA group and abundance filter + fluidRow( + column(width = 7, + div(style="float:left", + h4("MS\u00B9 abundance filter for HCA") + ) + ),##column + column(width = 5, + div(style="float:right", + bsTooltip(id = "showHCAfilterOptions", title = "Display filter settings", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showHCAfilterOptions", label = "Show filter settings", value = TRUE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showHCAfilterOptions", + bsTooltip(id = "hcaFilter_average", title = "The average MS\u00B9 abundance should be greater or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "hcaFilter_average", placeholder = 'E.g. 10000', label = "Average MS\u00B9 abundance"), + bsTooltip(id = "hcaFilter_lfc", title = "The log2-fold change [ log2( mean(group one) / mean(group two) ) ] between the average MS\u00B9 abundances should be greater/smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "hcaFilter_lfc", placeholder = 'E.g. 2 or -2', label = "MS\u00B9 log2-fold change"), + fluidRow(style = "overflow-y:scroll; + max-height: 200px", + #border: 1px solid #cccccc; + column( + width = 6, + tags$div( + title="Please select the first sample group", + radioButtons(inputId = "hcaFilterGroupOne", label = "Group 1", choices = c("")) + ) + ), + column( + width = 6, + tags$div( + title="Please select the second sample group", + radioButtons(inputId = "hcaFilterGroupTwo", label = "Group 2", choices = c("")) + ) + ) + ), + bsTooltip(id = "hcaFilterIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "hcaFilterIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), + ############################################################################################## + ## filter button + fluidRow( + column(width = 6, + div(style="float:left;width:100%", + bsTooltip(id = "applyHcaFilters", title = "Press to determine the set of MS\u00B9 features which fulfill the given filter criteria", placement = "bottom", trigger = "hover"), + actionButton(inputId = "applyHcaFilters", label = "Apply filter", class="btn-success", width = "100%") + ) + ),##column + column(width = 6, + div(style="float:right;width:100%", + bsTooltip(id = "clearHcaFilters", title = "Press to clear the MS\u00B9 abundance filter for HCA", placement = "bottom", trigger = "hover"), + actionButton(inputId = "clearHcaFilters", label = "Clear filter", class="btn-danger", width = "100%") + ) + )##column + )##row + ),## conditional panel + # ),##well panel + # wellPanel( + hr(), + h4("Filtered MS\u00B9 features"), + bsTooltip(id = "hcaFilteredPrecursors", title = paste("The number of MS\u00B9 features which fulfill the given filter criteria. HCA analysis is only possible for less than", + 5000, #maximumNumberOfPrecursorsForHca, + "MS\u00B9 features."), + placement = "bottom", trigger = "hover"), + verbatimTextOutput("hcaFilteredPrecursors"), + conditionalPanel( + condition = "output.hcaFilterValid", + bsTooltip(id = "downloadHcaFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), + downloadButton('downloadHcaFilteredPrecursors', 'Download reduced project file') + )##conditional + ),##well panel + conditionalPanel( + condition = "output.hcaFilterValid", + wellPanel( + ############################################################################################## + ## HCA properties + fluidRow( + column(width = 6, + div(style="float:left", + h4("HCA properties") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "showHCAadvancedOptions", title = "Display further HCA settings", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "showHCAadvancedOptions", label = "Show advanced options", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.showHCAadvancedOptions", + bsTooltip(id = "hcaDistanceFunction", title = "The distance function used for clustering", placement = "bottom", trigger = "hover"), + selectInput(multiple = FALSE, inputId = "hcaDistanceFunction", label = "Distance function", selected = "Jaccard (intensity-weighted)", choices = c( + "Jaccard", + "Jaccard (intensity-weighted)", + "Jaccard (fragment-count-weighted)", + "NDP (Normalized dot product)" + ), selectize = FALSE) + #bsTooltip(id = "hcaClusterMethod", title = "The method used for clustering", placement = "bottom", trigger = "hover"), + #selectInput(multiple = FALSE, inputId = "hcaClusterMethod", label = "Cluster method", selected = "ward.D", choices = c( + # "single", + # "complete", + # "average", + # "mcquitty", + # "median", + # "centroid", + # "ward.D", + # "ward.D2" + #), selectize = FALSE) + ), + fluidRow( + column(width = 6, + bsTooltip(id = "drawHCAplots", title = "Display the HCA dendrogram given the set of filtered MS\u00B9 features and HCA settings", placement = "bottom", trigger = "hover"), + actionButton(inputId = "drawHCAplots", label = "Draw hierarchical cluster", class="btn-success", width = "100%") + ),##column + column(width = 6 + + )##column + ),##row + conditionalPanel( + condition = "output.showGUI && output.plotHcaShown", + br(), + bsTooltip(id = "downloadDistanceMatrix", title = "Download the distance matrix of the currently displayed hierarchical cluster dendrogram", placement = "bottom", trigger = "hover"), + downloadButton('downloadDistanceMatrix', 'Download distance matrix') + ) + )## well panel + )## conditional panel + ),## conditional panel + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + ),## conditional panel + conditionalPanel( + condition = "output.showGUI && !output.globalMS2filterValid", + wellPanel( + h4("Please apply a valid MS/MS filter") + )## well panel + )## conditional panel + ),## tab panel + ############################################################################################## + ############################################################################################## + ## search + tabPanel( + title = "Search", + conditionalPanel( + condition = "output.showGUI && (output.plotHcaShown || output.plotPcaShown)", + #condition = "output.showGUI", + wellPanel( + h4("Search mode"), + bsTooltip(id = "searchMS1orMS2", title = "Please choose the criterion for selecting MS\u00B9 features", placement = "bottom", trigger = "hover"), + radioButtons(inputId = "searchMS1orMS2", label = NULL, choices = c("MS1 feature m/z", "Fragment m/z")), + hr(), + conditionalPanel( + condition = "input.searchMS1orMS2 == 'MS1 feature m/z'", + fluidRow( + column(width = 6, + bsTooltip(id = "searchMS1mass", title = "The MS\u00B9 feature m/z should be similar to at least one of the given values (separated by \",\")", placement = "bottom", trigger = "hover"), + textInput(inputId = "searchMS1mass", placeholder = 'E.g. 592.1792', label = "MS\u00B9 feature m/z('s)") + ),##column + column(width = 6, + bsTooltip(id = "searchMS1massPpm", title = "The specified MS\u00B9 feature m/z allows this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "searchMS1massPpm", placeholder = 'PPM number here', label = "PPM") + )##column + )##row + ),## conditional panel + conditionalPanel( + condition = "input.searchMS1orMS2 == 'Fragment m/z'", + fluidRow( + column(width = 11, + bsTooltip(id = "search_ms2_masses1", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "search_ms2_masses1", placeholder = 'E.g. 161.0443', label = "MS/MS spectrum includes mass(es) #1") + ), + column(width = 1, + h4("or") + ) + ), + fluidRow( + column(width = 11, + bsTooltip(id = "search_ms2_masses2", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "search_ms2_masses2", placeholder = 'E.g. -88.01808', label = "MS/MS spectrum includes mass(es) #2") + ), + column(width = 1, + h4("or") + ) + ), + fluidRow( + column(width = 11, + bsTooltip(id = "search_ms2_masses3", title = "The MS/MS spectra should include the following fragment / neutral loss mass(es) (separated by \",\")

E.g. \"96.969, -162.053\" for a compound with a phosphate - fragment (H2PO4-) and a hexose - neutral loss (C6O5H10)", placement = "bottom", trigger = "hover"), + textInput(inputId = "search_ms2_masses3", placeholder = 'E.g. 96.969, -162.053', label = "MS/MS spectrum includes mass(es) #3") + ), + column(width = 1, + h4("") + ) + ), + bsTooltip(id = "searchMS2massPpm", title = "The specified fragment m/z values allow this error in PPM (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "searchMS2massPpm", placeholder = 'PPM number here', label = "PPM") + ),## conditional panel + bsTooltip(id = "searchIncludeIgnoredPrecursors", title = "Include or filter out ignored MS\u00B9 features, i.e. MS\u00B9 features which have been annotated as \\'Ignore\\'", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "searchIncludeIgnoredPrecursors", label = "Include ignored MS\u00B9 features", value = FALSE), + fluidRow( + column(width = 6, + div(style="float:left;width:100%", + bsTooltip(id = "applySearch", title = "Press to mark the set of MS\u00B9 features which fulfill the given criteria", placement = "bottom", trigger = "hover"), + actionButton(inputId = "applySearch", label = "Search", class="btn-success", width = "100%") + ) + ),##column + column(width = 6, + div(style="float:right;width:100%", + bsTooltip(id = "clearSearch", title = "Press to clear the selected set of MS\u00B9 feature hits in HCA and PCA", placement = "bottom", trigger = "hover"), + actionButton(inputId = "clearSearch", label = "Clear search", class="btn-danger", width = "100%") + ) + )##column + ),##row + hr(), + h4("MS\u00B9 feature hits"), + bsTooltip(id = "searchInfo", title = "The number of MS\u00B9 features which fulfill the given filter criteria", placement = "bottom", trigger = "hover"), + verbatimTextOutput("searchInfo"), + conditionalPanel( + condition = "output.searchFilterValid & output.filterSearchActive", + bsTooltip(id = "downloadSearchPrecursors", title = "Download a project file which is reduced to the searched set of MS\u00B9 features", placement = "bottom", trigger = "hover"), + downloadButton('downloadSearchPrecursors', 'Download reduced project file') + )##conditional + )##well + ),## conditional panel + conditionalPanel( + #condition = "!(output.analysisType == 'HCA' || output.analysisType == 'PCA')", + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well + ),## conditional panel + conditionalPanel( + condition = "output.showGUI && !(output.plotHcaShown || output.plotPcaShown)", + wellPanel( + h4("Please perform HCA or PCA prior to search") + )## well + )## conditional panel + ),## tab panel + tabPanel( + title = "Classifiers", + conditionalPanel( + condition = "output.showGUI", + wellPanel( + h4("Classifier selection"), + bsTooltip(id = "classifierCount", title = "The number of available classifiers for the semi-automated metabolite family annotation of MS\u00B9 features", placement = "bottom", trigger = "hover"), + verbatimTextOutput(outputId = "classifierCount"), + DT::dataTableOutput("classifierSelectionTable"), + bsTooltip(id = "doAnnotation", title = "Press to automatically annotate metabolite families to spectra ", placement = "bottom", trigger = "hover"), + disabled(actionButton(inputId = "doAnnotation", label = "Perform scan", class="btn-success", width = "100%")) + ) + ), + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + )## conditional panel + ),## tab panel + tabPanel( + title = "Annotations", + conditionalPanel( + condition = "output.showGUI", + wellPanel( + h4("Metabolite family selection"), + bsTooltip(id = "familyCount2", title = "The number of available metabolite families which were annotated among the MS\u00B9 features", placement = "bottom", trigger = "hover"), + verbatimTextOutput(outputId = "familyCount2"), + DT::dataTableOutput("familySelectionTable"), + conditionalPanel( + condition = "output.metaboliteFamilySelected", + #condition = "length(input$familySelectionTable_rows_selected) == 1", + h4("Metabolite family properties"), + bsTooltip(id = "featureCountForFamily", title = "The number of MS\u00B9 features of the selected metabolite family", placement = "bottom", trigger = "hover"), + verbatimTextOutput(outputId = "featureCountForFamily"), + fluidRow( + column(width = 4, + bsTooltip(id = "selectMetaboliteFamily", title = "Press to select this metabolite family", placement = "bottom", trigger = "hover"), + actionButton(inputId = "selectMetaboliteFamily", label = "Select", class="btn-success", width = "100%") + ),##column + column(width = 4, + bsTooltip(id = "renameMetaboliteFamily", title = "Press to rename this metabolite family annotation", placement = "bottom", trigger = "hover"), + actionButton(inputId = "renameMetaboliteFamily", label = "Rename", class="btn-success", width = "100%") + ),##column + column(width = 4, + bsTooltip(id = "removeMetaboliteFamily", title = "Press to remove this metabolite family annotation", placement = "bottom", trigger = "hover"), + actionButton(inputId = "removeMetaboliteFamily", label = "Remove", class="btn-danger", width = "100%") + )##column + ),##row + conditionalPanel( + condition = "output.classifierLoaded", + bsTooltip(id = "metaboliteFamilyComparisonClass", title = "Please choose the class for comparison", placement = "bottom", trigger = "hover"), + selectInput(multiple = FALSE, inputId = "metaboliteFamilyComparisonClass", label = "Compare to class", selected = "[init]", choices = c("[init]"), selectize = FALSE) + ), + plotOutput(height = 250, + outputId = "fragmentPlot2", + #hover = "fragmentPlot2_hover", + hover = hoverOpts( + id = "fragmentPlot2_hover", + delay = 50, + delayType = "debounce" + ), + click = "fragmentPlot2_click", + dblclick = "fragmentPlot2_dblclick", + #brush = "fragmentPlot2_brush" + brush = brushOpts( + id = "fragmentPlot2_brush", + resetOnNew = TRUE, + direction = "x", + delay = 00, + delayType = "debounce" + ) + ), + DT::dataTableOutput("ms1FeatureTableForAnnotation"), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "downloadMetaboliteFamilyConsensusSpectrum", title = "Download the consensus spectrum for the selected metabolite family", placement = "bottom", trigger = "hover"), + downloadButton(outputId = "downloadMetaboliteFamilyConsensusSpectrum", label = "Download consensus spectrum"), + tags$style(type='text/css', "#downloadMetaboliteFamilyConsensusSpectrum { width:100%}") + ) + ),##column + column(width = 6, style="width:50%", + div(style="float:right;width:100%", + bsTooltip(id = "downloadMetaboliteFamilyFilteredPrecursors", title = "Download a project file which is reduced to the filtered set of MS\u00B9 features", placement = "bottom", trigger = "hover"), + downloadButton('downloadMetaboliteFamilyFilteredPrecursors', 'Download reduced project file'), + tags$style(type='text/css', "#downloadMetaboliteFamilyFilteredPrecursors { width:100%}") + ) + )##column + )##row + )##conditional + )##well + ),##conditional + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + )## conditional panel + ),## tab panel + tabPanel( + title = "Project", + conditionalPanel( + condition = "output.showGUI", + wellPanel( + h4("MetFamily project"), + fluidRow( + column(width = 6, div(style="float:left;width:100%", + h5("Project name") + )),##column + column(width = 6, div(style="float:right;width:100%", + bsTooltip(id = "projectName2", title = "The name of the project", placement = "bottom", trigger = "hover"), + textInput(inputId = "projectName2", label = NULL, value = "", width = "100%") + ))##column + ),##row + fluidRow( + column(width = 6, div(style="float:left;width:100%", + h5("Project description") + )),##column + column(width = 6, div(style="float:right;width:100%", + bsTooltip(id = "projectDescription2", title = "Please update the description of this project as free text", placement = "bottom", trigger = "hover"), + tags$style(type="text/css", "projectDescription2 {width:100%}"), + tags$textarea(id = 'projectDescription2', placeholder = 'Comments here', rows = 3, ""), + bsTooltip(id = "updateProjectDescription", title = "Press to update the project description", placement = "bottom", trigger = "hover"), + actionButton(inputId = "updateProjectDescription", label = "Update project description", class="btn-success", width = "100%") + ))##column + ),##row + fluidRow( + column(width = 6, + div(style="float:left", + h4("Data import parameters") + ) + ),##column + column(width = 6, + div(style="float:right", + bsTooltip(id = "displayImportParameters", title = "Display parameters used for the initial data import", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "displayImportParameters", label = "Display import parameters", value = FALSE) + ) + )##column + ),##row + conditionalPanel( + condition = "input.displayImportParameters", + h5("Fragment filter"), + fluidRow( + column(width = 6, + bsTooltip(id = "minimumIntensityOfMaximalMS2peak2", title = "A MS/MS spectrum is considered iff the MS/MS feature with maximum intensity is greater or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "minimumIntensityOfMaximalMS2peak2", label = "Min. spectrum intensity", value = 2000) + ),##column + column(width = 6, + bsTooltip(id = "minimumProportionOfMS2peaks2", title = "A MS/MS feature is considered iff the intensity is greater or equal than the maximum intensity times this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "minimumProportionOfMS2peaks2", label = "MS/MS peak proportion", value = 0.05) + )##column + ),##row + h5("Neutral losses"), + fluidRow( + column(width = 6, + bsTooltip(id = "neutralLossesPrecursorToFragments2", title = "Include neutral losses relative to the precursor ion, i.e. the m/z difference between the m/z of the precursor ion and the m/z of each fragment ion of the corresponding MS/MS spectrum", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "neutralLossesPrecursorToFragments2", label = "Fragment vs. precursor", value = TRUE) + ),##column + column(width = 6, + bsTooltip(id = "neutralLossesFragmentsToFragments2", title = "Include neutral losses amongst fragment ions, i.e. the m/z difference between the m/z values of all pairs of fragment ions within each MS/MS spectrum", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "neutralLossesFragmentsToFragments2", label = "Fragment vs. fragment", value = FALSE) + )##column + ),##row + h5("Fragment grouping"), + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_grouping2", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_grouping2", label = "m/z deviation (abs.)", value = 0.01) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_grouping2", title = "A MS/MS feature is added to a fragment group if the absolute m/z difference is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_grouping2", label = "m/z deviation (PPM)", value = 10) + )##column + ),##row + h4("Advanced parameters"), + h5("MS\u00B9 feature deisotoping"), + bsTooltip(id = "doPrecursorDeisotoping2", title = "If checked, the set of MS\u00B9 features is deisotoped", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "doPrecursorDeisotoping2", label = "MS\u00B9 feature deisotoping done", value = TRUE), + conditionalPanel( + condition = "input.doPrecursorDeisotoping2", + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_precursorDeisotoping2", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value (analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_precursorDeisotoping2", label = "m/z deviation (abs.)", value = 0.01) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_precursorDeisotoping2", title = "A MS\u00B9 feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million, analog for the +2 isotopic peak)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_precursorDeisotoping2", label = "m/z deviation (PPM)", value = 10) + )##column + )##row + ),##conditional + bsTooltip(id = "maximumRtDifference2", title = "A MS\u00B9 feature is considered an isotopic peak if the absolute of the retention time difference to the (putative) monoisotopic peak is smaller or equal than this value (in minutes)", placement = "bottom", trigger = "hover"), + textInput(inputId = "maximumRtDifference2", label = "Retention time difference", value = 0.02), + h5("Fragment deisotoping"), + bsTooltip(id = "doMs2PeakGroupDeisotoping2", title = "If checked, the set of MS/MS features is deisotoped", placement = "bottom", trigger = "hover"), + checkboxInput(inputId = "doMs2PeakGroupDeisotoping2", label = "Fragment deisotoping done", value = TRUE), + conditionalPanel( + condition = "input.doMs2PeakGroupDeisotoping2", + fluidRow( + column(width = 6, + bsTooltip(id = "mzDeviationAbsolute_ms2PeakGroupDeisotoping2", title = "_A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than this value", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping2", label = "m/z deviation (abs.)", value = 0.01) + ),##column + column(width = 6, + bsTooltip(id = "mzDeviationInPPM_ms2PeakGroupDeisotoping2", title = "A MS/MS feature is considered an +1 isotopic peak if the absolute of the m/z difference to the (putative) monoisotopic peak minus 1.0033548378 (=13C - 12C) is smaller or equal than the m/z times this value divided by 1,000,000 (parts per million)", placement = "bottom", trigger = "hover"), + textInput(inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping2", label = "m/z deviation (PPM)", value = 10) + )##column + )##row + )##conditional + ),##conditional + h4("Export"), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "prepareAllPrecursors", title = "Download the full project file", placement = "bottom", trigger = "hover"), + actionButton("prepareAllPrecursors", "Project export", icon = icon("file-export", lib = "font-awesome"), style="width:100%"), + tags$style(type='text/css', "#downloadAllPrecursors { width:100%}") + ) + ), #column + column(width = 6, style="width:50%", + div(style="float:right;width:100%", + bsTooltip(id = "downloadImportParameterSet", title = "Download a parameter file with the parameters which have been used for the initial data import", placement = "bottom", trigger = "hover"), + downloadButton(outputId = "downloadImportParameterSet", label = "Export import parameter set"), + tags$style(type='text/css', "#downloadImportParameterSet { width:100%}") + ) + )##column + ),##row + br(), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "downloadPcaImage", title = "Download the currently displayed PCA plots as image", placement = "bottom", trigger = "hover"), + downloadButton('downloadPcaImage', 'Export PCA as image'), + tags$style(type='text/css', "#downloadPcaImage { width:100%}") + ) + ),##column + column(width = 6, style="width:50%", + div(style="float:right;width:100%", + bsTooltip(id = "downloadPcaImageType", title = "The user is able to download the PCA plot as image of different types: Portable Network Graphics (*.png) file, Scalable Vector Graphics (*.svg) file, Portable Document Format (*.pdf) file", placement = "bottom", trigger = "hover"), + radioButtons(inputId = "downloadPcaImageType", label = NULL, choices = c("png", "svg", "pdf"), selected = "png", inline = TRUE, width = "100%") + ) + )##column + ),##row + br(), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "downloadHcaImage", title = "Download the currently displayed HCA plots as image", placement = "bottom", trigger = "hover"), + downloadButton('downloadHcaImage', 'Export HCA as image'), + tags$style(type='text/css', "#downloadHcaImage { width:100%}") + ) + ),##column + column(width = 6, style="width:50%", + div(style="float:right;width:100%", + bsTooltip(id = "downloadHcaImageType", title = "The user is able to download the HCA plot as image of different types: Portable Network Graphics (*.png) file, Scalable Vector Graphics (*.svg) file, Portable Document Format (*.pdf) file", placement = "bottom", trigger = "hover"), + radioButtons(inputId = "downloadHcaImageType", label = NULL, choices = c("png", "svg", "pdf"), selected = "png", inline = TRUE, width = "100%") + ) + )##column + ),##row + br(), + fluidRow( + column(width = 6, style="width:50%", + div(style="float:left;width:100%", + bsTooltip(id = "downloadReport", title = "Download the currently displayed HCA plots and PCA plots as report", placement = "bottom", trigger = "hover"), + downloadButton('downloadReport', 'Export analysis report'), + tags$style(type='text/css', "#downloadReport { width:100%}") + ) + ),##column + column(width = 6, style="width:50%", + div(style="float:right;width:100%" + ## nothing here + ) + )##column + )##row + )##well + ),## conditional panel + conditionalPanel( + condition = "!output.showGUI", + wellPanel( + h4("Please import a data file") + )## well panel + )## conditional panel + )## tab panel + )## tab set panel + )## column + ),##conditional + ############################################################################################## + ############################################################################################## + ############################################################################################## + ## plots + #uiOutput("runRightColumn") + source(file = "app_files/ui_rightColumn.R", local = TRUE)$value + ),## tab + ########################################################################################## + ########################################################################################## + ########################################################################################## + ########################################################################################## + ## tab about + tabPanel( + title = "About", + ############################################################################################## + ## intro + wellPanel( + h4(HTML("MetFamily 1.0")), + fluidRow( + column(width = 9, + helpText( + "The MetFamily web application is designed for the identification of regulated metabolite families. This is possible on the basis of metabolite profiles for a set of MS\u00B9 features as well as one MS/MS spectrum for each MS\u00B9 feature. Group-discriminating MS\u00B9 features are identified using a principal component analysis (PCA) of metabolite profiles and metabolite families are identified using a hierarchical cluster analysis (HCA) of MS/MS spectra. Regulated metabolite families are identified by considering group-discriminating MS\u00B9 features from corporate metabolite families." + ) + ),##column + column(width = 3, + tags$a(imageOutput(outputId = "ipbImage", width = "100%", height = "100%"), href='http://www.ipb-halle.de/en/', target='_blank') + #HTML("") + )##column + )## row + ),## well panel + wellPanel( + h4(HTML("Published in Analytical Chemistry (ACS Publications):")), + br(), + h5(HTML("Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies")), + p(HTML("Hendrik Treutler1, Hiroshi Tsugawa2, Andrea Porzel3, Karin Gorzolka1, Alain Tissier4, Steffen Neumann1, and Gerd Ulrich Balcke4*")), + p(HTML(paste( + "", + "1Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, D-06120 Halle/Saale, Germany", "
", + "2RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan", "
", + "3Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle/Saale, Germany", "
", + "4Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Weinberg 3, D-06120 Halle/Saale, Germany", "
", + "*Corresponding author: Gerd Ulrich Balcke Gerd.Balcke@ipb-halle.de + ", sep="" + ))), + br(), + h5(HTML("Abstract")), + p(HTML("The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS\u00B9 abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application “MetFamily”, which is freely available at http://msbi.ipb-halle.de/MetFamily/. MetFamily provides a dynamic link between the patterns based on MS\u00B9-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS\u00B9 patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR.")), + br(), + h5(HTML("Cite")), + p(HTML(paste( + "Hendrik Treutler, Hiroshi Tsugawa, Andrea Porzel, Karin Gorzolka, Alain Tissier, Steffen Neumann, and Gerd Ulrich U. Balcke.
", + "Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.
", + "Analytical chemistry, 88(16):8082-8090, August 2016.
", + "doi:10.1021/acs.analchem.6b01569", + sep = ""))) + ),## well panel + wellPanel( + h4(HTML("Documentation")), + p(HTML("Please find a user guide for the usage of the MetFamily web application below. ")), + bsTooltip(id = "downloadDocUserGuide", title = "Download the user guide for the MetFamily web application", placement = "bottom", trigger = "hover"), + downloadButton('downloadDocUserGuide', 'Download user guide'), + p(HTML("We provide a specification of the input file format. In the MetFamily publication we demonstrated the usage of MetFamily with UPLC-(-)ESI-SWATH-MS/MS data preprocessed with MS-DIAL. In the input specification, however, we demonstrate the generation of these files with GC-EI-MS data processed with xcms and CAMERA We also analyzed idMSMS spectra and LC-MS/MS spectra from DDA in MetFamily.")), + bsTooltip(id = "downloadDocInputSpecification", title = "Download the input specification of the MetFamily web application", placement = "bottom", trigger = "hover"), + downloadButton('downloadDocInputSpecification', 'Download input specification') + ),## well panel + wellPanel( + h4(HTML("Feedback")), + p(HTML("The MetFamily web application is designed to support researchers in the interpretation of comparative metabolomics studies at the level of metabolite families. Please help to improve this tool by comments, bug reports, and feature requests. You can contact Dr. Gerd Balcke via EMail and issues on GitHub.")) + ),## well panel + wellPanel( + h4(HTML("Session info")), + verbatimTextOutput(outputId = "rInfo") + )## well panel + )## tab + )## navBar +)## shinyUI From 16e5129db6b42c0438ad9db3dbffb73a257badef Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:06:30 +0100 Subject: [PATCH 4/8] Added shinybusy #52 --- MetFamily/R/R_packages.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/MetFamily/R/R_packages.R b/MetFamily/R/R_packages.R index ea333d8..761152f 100755 --- a/MetFamily/R/R_packages.R +++ b/MetFamily/R/R_packages.R @@ -13,6 +13,8 @@ library("DT") library("colourpicker") #install.packages("shinyBS") library("shinyBS") +#install.packages("shinybusy") +library("shinybusy") ############################################################################################################## ## mass spectrometry From 381f25b3feb8e032e654e97cf237831a87593211 Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:07:13 +0100 Subject: [PATCH 5/8] Fixed #52 --- .../app_files/server_functionsDownloads.R | 25 +++++++++++++------ 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/MetFamily/app_files/server_functionsDownloads.R b/MetFamily/app_files/server_functionsDownloads.R index 0015bff..b5e7b47 100644 --- a/MetFamily/app_files/server_functionsDownloads.R +++ b/MetFamily/app_files/server_functionsDownloads.R @@ -230,10 +230,12 @@ writeTable <- function(precursorSet, file){ #gz1 <- gzfile(description = file, open = "w") #write.table(x = dataFrame, file = gz1, sep = "\t", row.names = FALSE, col.names = FALSE, quote = FALSE) #close(gz1) + show_modal_spinner(spin="scaling-squares", text="\nMerging project files to csv. This can take several minutes!") lines <- createExportMatrix(precursorSet) gz1 <- gzfile(description = file, open = "w") writeLines(text = lines, con = gz1) close(gz1) + remove_modal_spinner() } ## individual downloads output$downloadGlobalMS2filteredPrecursors <- downloadHandler( @@ -286,13 +288,22 @@ output$downloadSelectedPrecursors <- downloadHandler( }, contentType = 'text/csv' ) -output$downloadAllPrecursors <- downloadHandler( - filename = function() { - createExportMatrixName() - }, - content = function(file) { - precursorSet <- 1:dataList$numberOfPrecursors - writeTable(precursorSet = precursorSet, file = file) +#Obvserve button for exporting the project +observeEvent(input$prepareAllPrecursors, { + ExportMatrixName <<- createExportMatrixName() + precursorSet <- 1:dataList$numberOfPrecursors + writeTable(precursorSet = precursorSet, file = file.path(tempdir(),ExportMatrixName)) + showModal(modalDialog(title = "Download", footer = NULL, size="s", fluidRow(column(12, p("Your download is ready."))), + fluidRow(column(3,downloadButton(outputId = "downloadAllpreparedPrecursors", label = "Download project"))), +)) +}) +#Serving the modal with the download button to download the project +output$downloadAllpreparedPrecursors <- downloadHandler( + filename <- ExportMatrixName, + content = function(file){ + file.copy(file.path(tempdir(),ExportMatrixName), file) + file.remove(file.path(tempdir(),ExportMatrixName)) + removeModal() }, contentType = 'text/csv' ) From fe827dcb74371af1757e89668a7e35ee9c794a72 Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:07:32 +0100 Subject: [PATCH 6/8] Added shinybusy dependency #52 --- binder/install.R | 1 + 1 file changed, 1 insertion(+) diff --git a/binder/install.R b/binder/install.R index c3639ae..2ae34b7 100644 --- a/binder/install.R +++ b/binder/install.R @@ -6,6 +6,7 @@ install.packages("BiocManager") install.packages("shiny") devtools::install_github("rstudio/htmltools") install.packages("shinyjs") +install.packages("shinybusy") install.packages("DT") install.packages("colourpicker") install.packages("shinyBS") From 10a2298b8e648f7e4a81a14ba063b7932d6a56e3 Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 16:17:02 +0100 Subject: [PATCH 7/8] Added .gitignore --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5b6a065 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata From 3e41e23cdae91eb739e0309f9826253d7b7a99c0 Mon Sep 17 00:00:00 2001 From: culpinnis Date: Wed, 26 Feb 2020 20:21:30 +0100 Subject: [PATCH 8/8] Added loading message for slow machines. --- MetFamily/server.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/MetFamily/server.R b/MetFamily/server.R index fc795f8..fea7c4d 100755 --- a/MetFamily/server.R +++ b/MetFamily/server.R @@ -110,6 +110,7 @@ sourceTheCode() ## server-side logic of the Shiny app shinyServer( func = function(input, output, session) { + show_modal_spinner(spin = "self-building-square", text="Loading libraries") ######################################################################################### ######################################################################################### ## global variables per user @@ -217,6 +218,7 @@ shinyServer( ######################################################################################### ######################################################################################### ## observer + remove_modal_spinner() #Remove preparing message ## controls obsTabs <- observeEvent(input$runTabs, {