inst/shiny-apps/compMS2Explorer/ui.R
In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets
library(compMS2Miner)
library(DT)
library(shiny)
library(igraph)
library(rhandsontable)
shiny::shinyUI(shiny::fluidPage(
tags$style(type="text/css", ".recalculating { opacity: 1.0; }"),
shiny::titlePanel(title='Composite MS2 Explorer'),
shiny::fluidRow(shiny::column(width=2,
a(shiny::tags$img(src='compMS2MinerLogoTutorial.png', height=121, width=324), href='http://bit.ly/2nnPwL1', target="_blank"),
shiny::h4(shiny::tags$b("Search Options:")),
shiny::checkboxInput("All_Features", "All features", value=TRUE),
shiny::checkboxInput("specDBMatch", "spectral database matches", value=FALSE),
shiny::checkboxInput("inSilicoMatch", "in silico matches", value=FALSE),
helpText("N.B.: when All features selected ",
"mass-to-charge and retention time search",
"cannot be performed however results will",
'still be subset by substructure type(s)',
'if selected.',
'if spectral database or in silico matches',
'action button is selected only those',
'spectra matched to a spectral database',
'or in silico data will be returned.'),
shiny::textInput("mass_to_charge", label=shiny::tags$b("mass to charge ratio : "), value=447.3468),
shiny::numericInput("mass_accuracy", label=shiny::tags$b("mass accuracy (ppm) : "), value=10, min=0.1, max=10000, step=0.1),
shiny::textInput("retentionTime", label=shiny::tags$b("retention time (seconds) : "), value=876.2210),
shiny::numericInput("RTtolerance", label=shiny::tags$b("retention time tolerance (+/- seconds) : "), value=5, min=1, max=700, step=1),
shiny::selectInput("SubStrTypes", label=shiny::tags$b("substructure types to include (multiple combinations) :"), choices=c(" ", SubStrType.inputs), multiple=T),
shiny::selectInput("NotSubStrTypes", label=shiny::tags$b("substructure types to exclude (multiple combinations) :"), choices=c(" ", SubStrType.inputs), multiple=T),
shiny::selectInput("subStrAnnoTypes", label=shiny::tags$b("substructure type annotation (multiple combinations) :"), choices=c(" ", subStrAnno.inputs), multiple=T),
shiny::numericInput("subStrAnnoThresh", label=shiny::tags$b("summed relative intensity threshold (substructure type). "), value=10, min=0, max=1000, step=1),
shiny::actionButton("goButton", "Search")
#selectInput("Possible_contaminants", label=tags$b("Possible contaminant/false positive annotations to exclude (name_frequency) :"), choices=c(" ", as.character(AnnoFreq$name)), multiple=T),
),
shiny::column(width=2,
shiny::textInput("DB_match_name", "Or search for database matches by name", value="e.g. p-cresol"),
helpText("N.B.: substructure type(s) if selected and",
"mass-to-charge and retention time values",
'(if All features check-box unselected)',
"will also subset the data when searching",
'by database entry name'),
shiny::radioButtons("DB_match_table", 'Search in:', choices=c('DB Annotations', 'Best Annotations')),
shiny::actionButton("DBbutton", "Search"),
shiny::br(),
shiny::tags$b(shiny::tags$h4("network graphs")),
shiny::checkboxInput('firstNeigh', 'display first network neighbours only',
value = TRUE),
shiny::br(),
shiny::br(),
shiny::tags$b(shiny::tags$h4("metID comments")),
# render ui for move to comments table
shiny::br(),
# shiny::tags$b('move selected row from best annotation table to metID comments:'),
# shiny::actionButton("moveComments", "move"),
# shiny::br(),
# shiny::tags$b('Add selected annotation to Comments table:'),
# shiny::actionButton("addAnno", "addAnno"),
# shiny::br(),
shiny::tags$b('close app and save comments:'),
shiny::actionButton("CloseAppBtn", "Close"),
shiny::br(),
helpText("N.B.: make sure to assign the ",
"compMS2explorer output to an object",
'in your R session to save any metabolite',
"identification comments made ",
'by closing the application window',
'or by clicking the button below ',
'to end your session.',
'Published apps have read-only',
'metID comments tabs.'),
shiny::br(),
# download button corpus and PMIDs/ paper names
shiny::h5('Download zip file of PubMed papers, PMIDs and word frequencies (.txt)'),
shiny::downloadButton('downloadPubMedData', 'download'),
shiny::br(),
# shiny::tags$b("Save comments and best candidates"),
# shiny::actionButton("CommentButton", "SAVE"),
# shiny::br(),
# br(), br(), sliderInput("Loess_smooth", "Select the Loess smoother span :", min=0.01, max=1, value=0.66),
# numericInput("CorrCoefMin", "Minimum correlation coefficient :", min=0.3, max=0.99, value=0.3, step=0.01),
shiny::br(),
shiny::verbatimTextOutput('currEIC'),
shiny::uiOutput("FeatureNames"),
shiny::h5(shiny::textOutput("matchSummaryText")),
shiny::tableOutput("matchSummary"),
shiny::uiOutput("tabbedPanelButton"),
shiny::br(),
shiny::uiOutput("Plot_select")
),
shiny::column(width=8,
shiny::conditionalPanel(condition="input.tabbedPanelButton >'0' & input.FeatureNames!='No MS2 features found'",
shiny::tabsetPanel(shiny::tabPanel('Composite MS2 plot',
shiny::fluidRow(shiny::verbatimTextOutput("compMS2Hover")),
shiny::fluidRow(splitLayout(cellWidths = c('55%', '45%'), shiny::plotOutput("MS2_plot", width = "100%", height = "600px", brush = 'compMS2_brush', hover='compMS2_hover'), DT::dataTableOutput('spectralDBtable'))),
shiny::fluidRow(DT::dataTableOutput("compMS2tableInfo"))),
shiny::tabPanel('Overview plot',
shiny::fluidRow(shiny::plotOutput("overview_plot", width = "1000px", height = "600px", brush = 'overview_brush')),
shiny::fluidRow(DT::dataTableOutput("overviewtableInfo"))),
shiny::tabPanel('Correlation network plot', shiny::verbatimTextOutput("corrNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("corr_network_plot", height = "800px", brush = 'corr_network_brush'), DT::dataTableOutput("corrNetworkTableBrush"))),
shiny::tabPanel('Spectral similarity network plot', shiny::verbatimTextOutput("specSimNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("specSim_network_plot", height = "800px", brush = 'specSim_network_brush'), DT::dataTableOutput("specSimNetworkTableBrush"))),
shiny::tabPanel('Recon Substructure network plot', shiny::verbatimTextOutput("reconSubNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("reconSub_network_plot", height = "800px", brush = 'reconSub_network_brush'), DT::dataTableOutput("reconSubNetworkTableBrush"))),
# # shiny::tabPanel("Composite MS2 plot", rCharts::chartOutput("Raw_data_plot", "PolyCharts")), #, #plotOutput("MS2_plot", width = "800px", height = "600px")),
# shiny::tabPanel("MS2 spectrum table", DT::dataTableOutput(outputId="MS2_data")),
shiny::tabPanel("MS1 MS2 match summary", DT::dataTableOutput(outputId="metadata")),
shiny::tabPanel("DB Annotations", DT::dataTableOutput(outputId="DB.results")),
shiny::tabPanel("Best Annotations", DT::dataTableOutput("BestCandidates")),
shiny::tabPanel("Substructure Annotations", DT::dataTableOutput("BestSubStrAnno")),
# metId comments
shiny::tabPanel("metID comments", rHandsontableOutput("hot")),
# tabPanel("Best candidates", dataTableOutput("BestCandidate")),
shiny::tabPanel("PubMed Word Cloud",
shiny::fluidRow(shiny::verbatimTextOutput("WordCloudText")),
shiny::fluidRow(
splitLayout(shiny::splitLayout(
cellWidths = c(400, 550),
cellArgs = list(style = "padding: 6px"),#shiny::column(width=2,
shiny::uiOutput('customPubMedSearch'),
#shiny::column(width=2,
# shiny::uiOutput("nRandomArticles"),
shiny::uiOutput("nPMIDAbstracts")
))),
shiny::fluidRow(shiny::uiOutput("wordCloudSelect"),
shiny::uiOutput('pubMedSearchButton')),
shiny::br(),
shiny::fluidRow(splitLayout(cellWidths=c('40%', '60%'),
shiny::plotOutput("WordCloud", width = "800px", height = "600px"), DT::dataTableOutput(outputId="WordCloudTable")))
# shiny::fluidRow(shiny::uiOutput('downloadPubMedData'))
),
shiny::tabPanel("In silico fragmentation",
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
a(shiny::tags$h2('metFrag'), href='http://msbi.ipb-halle.de/MetFragBeta/', target="_blank"),
a(shiny::tags$h2('CFM'), href='http://cfmid.wishartlab.com/', target="_blank"))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
DT::dataTableOutput(outputId="metFragTable"), DT::dataTableOutput(outputId="cfmTable"))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
shiny::plotOutput(outputId = 'metFragPlot', width = "100%", height = "500px", brush='metFrag_brush'),
shiny::plotOutput(outputId = 'cfmPlot', width = "100%", height = "500px", brush='cfm_brush'))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
DT::dataTableOutput(outputId = 'metFragFragments'), DT::dataTableOutput(outputId = 'cfmFragments')))),
shiny::tabPanel('Predicted retention time plot', shiny::plotOutput(outputId = 'rtPredPlot', brush = 'rtPredPlot_brush', width = "100%", height = "600px"),
DT::dataTableOutput('rtPredTable', width = "100%", height = "600px")),
shiny::tabPanel("Tutorial videos", #t,
shiny::fluidRow(
tags$img(src='compMS2MinerLogo.png', height=121, width=324)),
shiny::fluidRow(tags$video(src='dynamicNoiseFilterVideo.mp4', type='video/mp4', controls='controls')),
shiny::fluidRow(tags$video(src='optimConsensusAnimation.mp4', type='video/mp4', controls='controls'))),
shiny::tabPanel("App construction pdf", shiny::htmlOutput('pdfviewer')),
shiny::tabPanel('App session info', shiny::htmlOutput('sessionTxt'))
#, tableOutput(outputId="SubStr_type")),
# shiny::tabPanel("InterFeature Correlation"), #, chartOutput("InterFeatureCorr", "morris")), #uiOutput("CorrCoefMin"),
# shiny::tabPanel("Chemical Similarity Scores"), #uiOutput("Compound"), uiOutput("IntraInter"), chartOutput("ChemicalSimilarity", "morris")),
# shiny::tabPanel("Comments"), #, shiny::uiOutput("CommentSectionHeader"), shiny::uiOutput("UserComments"))#, uiOutput("CommentButtonUI")
# shiny::tabPanel("LogD RT plot")#, uiOutput("RTwindow"), chartOutput("LogD_RT_plot", "PolyCharts"))
))
))
# fluidRow(column(h4(paste0("Results summary ", "(nMatches=", TotalFeatures, ", nCompositeSpectra=", TotalCompSpectra, ")")), width=6,
# dataTableOutput("MS2_features_detected")))
)) # end CompMS2 shiny UI
WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(compMS2Miner)
library(DT)
library(shiny)
library(igraph)
library(rhandsontable)
shiny::shinyUI(shiny::fluidPage(
tags$style(type="text/css", ".recalculating { opacity: 1.0; }"),
shiny::titlePanel(title='Composite MS2 Explorer'),
shiny::fluidRow(shiny::column(width=2,
a(shiny::tags$img(src='compMS2MinerLogoTutorial.png', height=121, width=324), href='http://bit.ly/2nnPwL1', target="_blank"),
shiny::h4(shiny::tags$b("Search Options:")),
shiny::checkboxInput("All_Features", "All features", value=TRUE),
shiny::checkboxInput("specDBMatch", "spectral database matches", value=FALSE),
shiny::checkboxInput("inSilicoMatch", "in silico matches", value=FALSE),
helpText("N.B.: when All features selected ",
"mass-to-charge and retention time search",
"cannot be performed however results will",
'still be subset by substructure type(s)',
'if selected.',
'if spectral database or in silico matches',
'action button is selected only those',
'spectra matched to a spectral database',
'or in silico data will be returned.'),
shiny::textInput("mass_to_charge", label=shiny::tags$b("mass to charge ratio : "), value=447.3468),
shiny::numericInput("mass_accuracy", label=shiny::tags$b("mass accuracy (ppm) : "), value=10, min=0.1, max=10000, step=0.1),
shiny::textInput("retentionTime", label=shiny::tags$b("retention time (seconds) : "), value=876.2210),
shiny::numericInput("RTtolerance", label=shiny::tags$b("retention time tolerance (+/- seconds) : "), value=5, min=1, max=700, step=1),
shiny::selectInput("SubStrTypes", label=shiny::tags$b("substructure types to include (multiple combinations) :"), choices=c(" ", SubStrType.inputs), multiple=T),
shiny::selectInput("NotSubStrTypes", label=shiny::tags$b("substructure types to exclude (multiple combinations) :"), choices=c(" ", SubStrType.inputs), multiple=T),
shiny::selectInput("subStrAnnoTypes", label=shiny::tags$b("substructure type annotation (multiple combinations) :"), choices=c(" ", subStrAnno.inputs), multiple=T),
shiny::numericInput("subStrAnnoThresh", label=shiny::tags$b("summed relative intensity threshold (substructure type). "), value=10, min=0, max=1000, step=1),
shiny::actionButton("goButton", "Search")
#selectInput("Possible_contaminants", label=tags$b("Possible contaminant/false positive annotations to exclude (name_frequency) :"), choices=c(" ", as.character(AnnoFreq$name)), multiple=T),
),
shiny::column(width=2,
shiny::textInput("DB_match_name", "Or search for database matches by name", value="e.g. p-cresol"),
helpText("N.B.: substructure type(s) if selected and",
"mass-to-charge and retention time values",
'(if All features check-box unselected)',
"will also subset the data when searching",
'by database entry name'),
shiny::radioButtons("DB_match_table", 'Search in:', choices=c('DB Annotations', 'Best Annotations')),
shiny::actionButton("DBbutton", "Search"),
shiny::br(),
shiny::tags$b(shiny::tags$h4("network graphs")),
shiny::checkboxInput('firstNeigh', 'display first network neighbours only',
value = TRUE),
shiny::br(),
shiny::br(),
shiny::tags$b(shiny::tags$h4("metID comments")),
# render ui for move to comments table
shiny::br(),
# shiny::tags$b('move selected row from best annotation table to metID comments:'),
# shiny::actionButton("moveComments", "move"),
# shiny::br(),
# shiny::tags$b('Add selected annotation to Comments table:'),
# shiny::actionButton("addAnno", "addAnno"),
# shiny::br(),
shiny::tags$b('close app and save comments:'),
shiny::actionButton("CloseAppBtn", "Close"),
shiny::br(),
helpText("N.B.: make sure to assign the ",
"compMS2explorer output to an object",
'in your R session to save any metabolite',
"identification comments made ",
'by closing the application window',
'or by clicking the button below ',
'to end your session.',
'Published apps have read-only',
'metID comments tabs.'),
shiny::br(),
# download button corpus and PMIDs/ paper names
shiny::h5('Download zip file of PubMed papers, PMIDs and word frequencies (.txt)'),
shiny::downloadButton('downloadPubMedData', 'download'),
shiny::br(),
# shiny::tags$b("Save comments and best candidates"),
# shiny::actionButton("CommentButton", "SAVE"),
# shiny::br(),
# br(), br(), sliderInput("Loess_smooth", "Select the Loess smoother span :", min=0.01, max=1, value=0.66),
# numericInput("CorrCoefMin", "Minimum correlation coefficient :", min=0.3, max=0.99, value=0.3, step=0.01),
shiny::br(),
shiny::verbatimTextOutput('currEIC'),
shiny::uiOutput("FeatureNames"),
shiny::h5(shiny::textOutput("matchSummaryText")),
shiny::tableOutput("matchSummary"),
shiny::uiOutput("tabbedPanelButton"),
shiny::br(),
shiny::uiOutput("Plot_select")
),
shiny::column(width=8,
shiny::conditionalPanel(condition="input.tabbedPanelButton >'0' & input.FeatureNames!='No MS2 features found'",
shiny::tabsetPanel(shiny::tabPanel('Composite MS2 plot',
shiny::fluidRow(shiny::verbatimTextOutput("compMS2Hover")),
shiny::fluidRow(splitLayout(cellWidths = c('55%', '45%'), shiny::plotOutput("MS2_plot", width = "100%", height = "600px", brush = 'compMS2_brush', hover='compMS2_hover'), DT::dataTableOutput('spectralDBtable'))),
shiny::fluidRow(DT::dataTableOutput("compMS2tableInfo"))),
shiny::tabPanel('Overview plot',
shiny::fluidRow(shiny::plotOutput("overview_plot", width = "1000px", height = "600px", brush = 'overview_brush')),
shiny::fluidRow(DT::dataTableOutput("overviewtableInfo"))),
shiny::tabPanel('Correlation network plot', shiny::verbatimTextOutput("corrNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("corr_network_plot", height = "800px", brush = 'corr_network_brush'), DT::dataTableOutput("corrNetworkTableBrush"))),
shiny::tabPanel('Spectral similarity network plot', shiny::verbatimTextOutput("specSimNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("specSim_network_plot", height = "800px", brush = 'specSim_network_brush'), DT::dataTableOutput("specSimNetworkTableBrush"))),
shiny::tabPanel('Recon Substructure network plot', shiny::verbatimTextOutput("reconSubNodesEdges"), splitLayout(cellWidths = c('70%', '30%'), shiny::plotOutput("reconSub_network_plot", height = "800px", brush = 'reconSub_network_brush'), DT::dataTableOutput("reconSubNetworkTableBrush"))),
# # shiny::tabPanel("Composite MS2 plot", rCharts::chartOutput("Raw_data_plot", "PolyCharts")), #, #plotOutput("MS2_plot", width = "800px", height = "600px")),
# shiny::tabPanel("MS2 spectrum table", DT::dataTableOutput(outputId="MS2_data")),
shiny::tabPanel("MS1 MS2 match summary", DT::dataTableOutput(outputId="metadata")),
shiny::tabPanel("DB Annotations", DT::dataTableOutput(outputId="DB.results")),
shiny::tabPanel("Best Annotations", DT::dataTableOutput("BestCandidates")),
shiny::tabPanel("Substructure Annotations", DT::dataTableOutput("BestSubStrAnno")),
# metId comments
shiny::tabPanel("metID comments", rHandsontableOutput("hot")),
# tabPanel("Best candidates", dataTableOutput("BestCandidate")),
shiny::tabPanel("PubMed Word Cloud",
shiny::fluidRow(shiny::verbatimTextOutput("WordCloudText")),
shiny::fluidRow(
splitLayout(shiny::splitLayout(
cellWidths = c(400, 550),
cellArgs = list(style = "padding: 6px"),#shiny::column(width=2,
shiny::uiOutput('customPubMedSearch'),
#shiny::column(width=2,
# shiny::uiOutput("nRandomArticles"),
shiny::uiOutput("nPMIDAbstracts")
))),
shiny::fluidRow(shiny::uiOutput("wordCloudSelect"),
shiny::uiOutput('pubMedSearchButton')),
shiny::br(),
shiny::fluidRow(splitLayout(cellWidths=c('40%', '60%'),
shiny::plotOutput("WordCloud", width = "800px", height = "600px"), DT::dataTableOutput(outputId="WordCloudTable")))
# shiny::fluidRow(shiny::uiOutput('downloadPubMedData'))
),
shiny::tabPanel("In silico fragmentation",
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
a(shiny::tags$h2('metFrag'), href='http://msbi.ipb-halle.de/MetFragBeta/', target="_blank"),
a(shiny::tags$h2('CFM'), href='http://cfmid.wishartlab.com/', target="_blank"))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
DT::dataTableOutput(outputId="metFragTable"), DT::dataTableOutput(outputId="cfmTable"))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
shiny::plotOutput(outputId = 'metFragPlot', width = "100%", height = "500px", brush='metFrag_brush'),
shiny::plotOutput(outputId = 'cfmPlot', width = "100%", height = "500px", brush='cfm_brush'))),
shiny::fluidRow(splitLayout(cellWidths=c('50%', '50%'),
DT::dataTableOutput(outputId = 'metFragFragments'), DT::dataTableOutput(outputId = 'cfmFragments')))),
shiny::tabPanel('Predicted retention time plot', shiny::plotOutput(outputId = 'rtPredPlot', brush = 'rtPredPlot_brush', width = "100%", height = "600px"),
DT::dataTableOutput('rtPredTable', width = "100%", height = "600px")),
shiny::tabPanel("Tutorial videos", #t,
shiny::fluidRow(
tags$img(src='compMS2MinerLogo.png', height=121, width=324)),
shiny::fluidRow(tags$video(src='dynamicNoiseFilterVideo.mp4', type='video/mp4', controls='controls')),
shiny::fluidRow(tags$video(src='optimConsensusAnimation.mp4', type='video/mp4', controls='controls'))),
shiny::tabPanel("App construction pdf", shiny::htmlOutput('pdfviewer')),
shiny::tabPanel('App session info', shiny::htmlOutput('sessionTxt'))
#, tableOutput(outputId="SubStr_type")),
# shiny::tabPanel("InterFeature Correlation"), #, chartOutput("InterFeatureCorr", "morris")), #uiOutput("CorrCoefMin"),
# shiny::tabPanel("Chemical Similarity Scores"), #uiOutput("Compound"), uiOutput("IntraInter"), chartOutput("ChemicalSimilarity", "morris")),
# shiny::tabPanel("Comments"), #, shiny::uiOutput("CommentSectionHeader"), shiny::uiOutput("UserComments"))#, uiOutput("CommentButtonUI")
# shiny::tabPanel("LogD RT plot")#, uiOutput("RTwindow"), chartOutput("LogD_RT_plot", "PolyCharts"))
))
))
# fluidRow(column(h4(paste0("Results summary ", "(nMatches=", TotalFeatures, ", nCompositeSpectra=", TotalCompSpectra, ")")), width=6,
# dataTableOutput("MS2_features_detected")))
)) # end CompMS2 shiny UI
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