Nothing
inst/LipidMSapp/ui.R
In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data
ui <- tagList(
navbarPage(
position = "fixed-top",
theme = shinythemes::shinytheme("flatly"),
title = div(img(src='iconohorizontal.png',style="margin-top: -14px; padding-right:0px; padding-left:0px; padding-bottom:10px", height = 60, width = 100)),
windowTitle = "LipidMS",
id = "inTabset",
tabPanel(title = "Data import", value = "tab1",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
sidebarPanel(width = 3,
fluidRow(textInput("jobname", "Job Name",
value = paste("Job", as.character(Sys.Date()), sep = "_")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(radioButtons("analysis", "How do you want to process your data?",
choices = c("Batch Processing" = "batch",
"Single Sample Processing" = "single"),
selected = "batch"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(column(4, textOutput("messageanalysis"), style="color:red")),
fluidRow(radioButtons("sI_polarity", "Polarity",
choices = c("Positive" = "positive",
"Negative" = "negative"),
selected = "positive"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("file1", "Choose mzXML File/s",
multiple = TRUE,
accept = c("text/plain",
".mzXML")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("metadata", "Metadata csv file",
multiple = TRUE,
accept = c("text/plain",
".csv")),
h6(em("It must be a csv file with 3 columns:\n",
"sample (mzXML file names),\n",
"acquisitionmode (MS, DIA or DDA) and\n",
"sampletype (QC, group1, group2, etc.)"), style = "color:grey"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("metadata", "Metadata csv file",
multiple = FALSE,
accept = c("text/plain",
".csv")),
h6(em("It must be a csv file with 3 columns:\n",
"sample (mzXML file names),\n",
"acquisitionmode (MS, DIA or DDA) and\n",
"sampletype (QC, group1, group2, etc.)"), style = "color:grey"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(column(4, h5(strong("sep")),
h6(em("column delimiter."), style = "color:grey")),
column(3, textInput("sep1", "", value=","))),
fluidRow(column(4, h5(strong("dec")),
h6(em("decimal character."), style = "color:grey")),
column(3, textInput("dec1", "", value="."))),
tags$hr(style = "border-color: white"),
fluidRow(actionButton("JumpTo2", "Next >", width = "100px"),
style = "margin: 20px 0px 0px 0px")
),
mainPanel(tableOutput("metadata"))
),
tabPanel(title = "Peak-picking", value = "tab2",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
tags$head(
tags$style(HTML("input[type=\"number\"] {
height: 35px; font-size:11px
}"))),
mainPanel(
position="left",
fluidRow(column(6, h5(strong("dmzagglom (in ppm)")),
h6(em("m/z tolerance used for partitioning and clustering. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzagglom_ms1", "MS1", value = 15, min = 0, max = 100, step = 1)),
column(3, numericInput("dmzagglom_ms2", "MS2", value = 15, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtagglom (in seconds)")),
h6(em("rt window used for partitioning (in seconds). 25 by default."), style = "color:grey")),
column(3, numericInput("drtagglom_ms1", "MS1", value = 500, min = 0, max = 1000, step = 1)),
column(3, numericInput("drtagglom_ms2", "MS2", value = 500, min = 0, max = 1000, step = 1))),
fluidRow(column(6, h5(strong("drtclust (in seconds)")),
h6(em("rt window used for clustering (in seconds). 25 by default."), style = "color:grey")),
column(3, numericInput("drtclust_ms1", "MS1", value = 100, min = 0, max = 1000, step = 1)),
column(3, numericInput("drtclust_ms2", "MS2", value = 200, min = 0, max = 1000, step = 1))),
fluidRow(column(6, h5(strong("minpeak")),
h6(em("minimum number of measurements required for a peak. By default, 5 for MS1 and 4 for MS2."), style = "color:grey")),
column(3, numericInput("minpeak_ms1", "MS1", value = 5, min = 1, max = 25, step = 1)),
column(3, numericInput("minpeak_ms2", "MS2", value = 4, min = 1, max = 25, step = 1))),
fluidRow(column(6, h5(strong("minint")),
h6(em("minimum intensity of a peak. By default, 1000 for MS1 and 100 for MS2."), style = "color:grey")),
column(3, numericInput("minint_ms1", "MS1", value = 1000, min = 0, max = 1e5, step = 1)),
column(3, numericInput("minint_ms2", "MS2", value = 100, min = 0, max = 1e5, step = 1))),
fluidRow(column(6, h5(strong("drtgap (in seconds)")),
h6(em("maximum rt gap length to be filled. 5 by default."), style = "color:grey")),
column(3, numericInput("drtgap_ms1", "MS1", value = 5, min = 0, max = 30, step = 1)),
column(3, numericInput("drtgap_ms2", "MS2", value = 5, min = 0, max = 30, step = 1))),
fluidRow(column(6, h5(strong("drtminpeak (in seconds)")),
h6(em("minimum rt width of a peak. 15 by default. At least minpeak within the drtminpeak window are required to define a peak."), style = "color:grey")),
column(3, numericInput("drtminpeak_ms1", "MS1", value = 15, min = 0, max = 500, step = 1)),
column(3, numericInput("drtminpeak_ms2", "MS2", value = 15, min = 0, max = 500, step = 1))),
fluidRow(column(6, h5(strong("drtmaxpeak (in seconds)")),
h6(em("maximum rt width of a single peak. 100 by default."), style = "color:grey")),
column(3, numericInput("drtmaxpeak_ms1", "MS1", value = 100, min = 0, max = 500, step = 1)),
column(3, numericInput("drtmaxpeak_ms2", "MS2", value = 200, min = 0, max = 500, step = 1))),
fluidRow(column(6, h5(strong("maxeicpeaks")),
h6(em("maximum number of peaks within one EIC. By default, 5 for 10 and 3 for MS2."), style = "color:grey")),
column(3, numericInput("recurs_ms1", "MS1", value = 5, min = 1, max = 50, step = 1)),
column(3, numericInput("recurs_ms2", "MS2", value = 10, min = 1, max = 50, step = 1))),
fluidRow(column(6, h5(strong("weight")),
h6(em("weight for assigning measurements to a peak. By default, 2 for MS1 and 3 for MS2."), style = "color:grey")),
column(3, numericInput("weight_ms1", "MS1", value = 2, min = 1, max = 10, step = 1)),
column(3, numericInput("weight_ms2", "MS2", value = 3, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("SN")),
h6(em("signal-to-noise ratio. By default, 3 for MS1 and 2 for MS2."), style = "color:grey")),
column(3, numericInput("sn_ms1", "MS1", value = 3, min = 1, max = 10, step = 1)),
column(3, numericInput("sn_ms2", "MS2", value = 2, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("SB")),
h6(em("signal-to-base ratio. By default, 3 for MS1 and 2 for MS2."), style = "color:grey")),
column(3, numericInput("sb_ms1", "MS1", value = 3, min = 1, max = 10, step = 1)),
column(3, numericInput("sb_ms2", "MS2", value = 2, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("dmzIso (in ppm)")),
h6(em("mass tolerance for isotope matching. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzIso_ms1", "MS1", value = 5, min = 0, max = 100, step = 1)),
column(3, numericInput("dmzIso_ms2", "MS2", value = 5, min = 0, max = 10, step = 1))),
fluidRow(column(6, h5(strong("drtIso")),
h6(em("rt window for isotope matching. 5 by default."), style = "color:grey")),
column(3, numericInput("drtIso_ms1", "MS1", value = 5, min = 0, max = 100, step = 1)),
column(3, numericInput("drtIso_ms2", "MS2", value = 5, min = 0, max = 100, step = 1))),
tags$hr(),
fluidRow(actionButton("GoBackTo1", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo3", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Batch processing", value = "tab3",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
tags$head(
tags$style(HTML("input[type=\"number\"] {
height: 35px; font-size:11px
}"))),
mainPanel(fluidRow(column(6, h5(strong("dmzalign")),
h6(em("mass tolerance between peak groups for alignment (in ppm). 5 by default."), style = "color:grey")),
column(3, numericInput("dmzalign", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtalign")),
h6(em("maximum rt distance between peaks for alignment (in seconds). 30 by default."), style = "color:grey")),
column(3, numericInput("drtalign", "", value = 30, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("span")),
h6(em("span parameter for loess rt smoothing. 0.4 by default."), style = "color:grey")),
column(3, numericInput("span", "", value = 0.4, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("minsamplesfracalign")),
h6(em("minimum samples fraction represented in each cluster used for alignment. 0.75 by default."), style = "color:grey")),
column(3, numericInput("minsamplesfracalign", "", value = 0.75, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("dmzgroup")),
h6(em("mass tolerance between peak groups for grouping (in ppm). 5 by default."), style = "color:grey")),
column(3, numericInput("dmzgroup", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtagglomgroup")),
h6(em("maximum rt distance in mz partitions for grouping (in seconds). 30 by default. It shouldn't be smaller than drtgroup."), style = "color:grey")),
column(3, numericInput("drtagglomgroup", "", value = 30, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("drtgroup")),
h6(em("maximum rt distance between peaks for grouping (in seconds). 30 by default."), style = "color:grey")),
column(3, numericInput("drtgroup", "", value = 15, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("minsamplesfracgroup")),
h6(em("minimum samples fraction represented in each cluster used for grouping. 0.25 by default."), style = "color:grey")),
column(3, numericInput("minsamplesfracgroup", "", value = 0.25, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("parallel")),
h6(em("parallelize processing. FALSE by default."), style = "color:grey")),
column(3, selectInput("parallel", "", choices = list("TRUE" = TRUE, "FALSE" = FALSE),
selected = FALSE))),
fluidRow(column(6, h5(strong("ncores")),
h6(em("number of cores to be used in case parallel is TRUE. 2 by default."), style = "color:grey")),
column(3, numericInput("ncores", "", value = 2, min = 0, max = 50, step = 1))),
tags$hr(),
fluidRow(actionButton("GoBackTo2", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo4", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Annotation", value = "tab4",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
mainPanel(fluidRow(column(6, h5(strong("dmzprecursor")),
h6(em("mass tolerance for precursor ions. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzprecursor", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("dmzproducts")),
h6(em("mass tolerance for product ions. 10 by default."), style = "color:grey")),
column(3, numericInput("dmzproducts", "", value = 10, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("rttol")),
h6(em("total rt window for coelution between precursor and product ions. 5 by default."), style = "color:grey")),
column(3, numericInput("rttol", "", value = 5, min = 0, max = 50, step = 1))),
fluidRow(column(6, h5(strong("coelcutoff")),
h6(em("coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. 0.7 by default."), style = "color:grey")),
column(3, numericInput("coelcutoff", "", value = 0.7, min = 0, max = 1, step = 0.05))),
tags$hr(),
fluidRow(column(6, checkboxGroupInput("lipidClassesPos", "Lipid classes to annotate for ESI+ :",
c("MG" = "MG",
"LPC" = "LPC",
"LPE" = "LPE",
"PC" = "PC",
"PCo" = "PCo",
"PCp" = "PCp",
"PE" = "PE",
"PEo" = "PEo",
"PEp" = "PEp",
"PG" = "PG",
"Sphingoid bases" = "Sph",
"Sphingoid bases phosphate" = "SphP",
"Cer" = "Cer",
"AcylCer" = "AcylCer",
"CerP" = "CerP",
"SM" = "SM",
"Carnitines" = "Carnitines",
"CE" = "CE",
"DG" = "DG",
"TG" = "TG"),
selected = c("MG", "LPC", "LPE", "PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG", "Sph",
"SphP", "Cer", "AcylCer", "CerP", "SM", "Carnitines", "CE", "DG", "TG"))),
column(6, checkboxGroupInput("lipidClassesNeg", "Lipid classes to annotate for ESI+ :",
c("FA" = "FA",
"FAHFA" = "FAHFA",
"LPC" = "LPC",
"LPE" = "LPE",
"LPG" = "LPG",
"LPI" = "LPI",
"LPS" = "LPS",
"PC" = "PC",
"PCo" = "PCo",
"PCp" = "PCp",
"PE" = "PE",
"PEo" = "PEo",
"PEp" = "PEp",
"PG" = "PG",
"PI" = "PI",
"PS" = "PS",
"Sphingoid bases" = "Sph",
"Sphingoid bases phosphate" = "SphP",
"Cer" = "Cer",
"AcylCer" = "AcylCer",
"CerP" = "CerP",
"CL" = "CL",
"Bile Acids" = "BA"),
selected = c("FA", "FAHFA", "LPC", "LPE", "LPG", "LPI", "LPS",
"PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG", "PI", "PS",
"Sph", "SphP", "Cer", "AcylCer", "CerP", "CL", "BA")))),
tags$hr(),
fluidRow(actionButton("GoBackTo3", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo5", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Run", value = "tab5",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
sidebarPanel(width = 3,
fluidRow(h5("\nRun your job: "),
style = "margin: 20px 0px 0px 0px"),
fluidRow(actionButton("do", "Run",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
tags$hr(style = "border-color: white"),
fluidRow(h5("\nDownload your results: "),
h6(em("(Wait until your results show up on the main panel)")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadSummary", "Summary Tables",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadPeaklist", "Annotated Peaklists",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadBatchResults", "Batch Results (if applied)",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadPlots", "Plots",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
tags$hr(style = "border-color: white"),
fluidRow(actionButton("GoBackTo4", "< Previous", width = "100px",
style="margin:40px 0px"),
style = "margin: 20px 0px 0px 0px")
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel("Summary Tables Annotation", tableOutput("summaryTable")),
tabPanel("Annotated Peaklists", tableOutput("annotatedPeaklist")),
tabPanel("Batch Results", tableOutput("features"))
)
))
)
)
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ui <- tagList(
navbarPage(
position = "fixed-top",
theme = shinythemes::shinytheme("flatly"),
title = div(img(src='iconohorizontal.png',style="margin-top: -14px; padding-right:0px; padding-left:0px; padding-bottom:10px", height = 60, width = 100)),
windowTitle = "LipidMS",
id = "inTabset",
tabPanel(title = "Data import", value = "tab1",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
sidebarPanel(width = 3,
fluidRow(textInput("jobname", "Job Name",
value = paste("Job", as.character(Sys.Date()), sep = "_")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(radioButtons("analysis", "How do you want to process your data?",
choices = c("Batch Processing" = "batch",
"Single Sample Processing" = "single"),
selected = "batch"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(column(4, textOutput("messageanalysis"), style="color:red")),
fluidRow(radioButtons("sI_polarity", "Polarity",
choices = c("Positive" = "positive",
"Negative" = "negative"),
selected = "positive"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("file1", "Choose mzXML File/s",
multiple = TRUE,
accept = c("text/plain",
".mzXML")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("metadata", "Metadata csv file",
multiple = TRUE,
accept = c("text/plain",
".csv")),
h6(em("It must be a csv file with 3 columns:\n",
"sample (mzXML file names),\n",
"acquisitionmode (MS, DIA or DDA) and\n",
"sampletype (QC, group1, group2, etc.)"), style = "color:grey"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(fileInput("metadata", "Metadata csv file",
multiple = FALSE,
accept = c("text/plain",
".csv")),
h6(em("It must be a csv file with 3 columns:\n",
"sample (mzXML file names),\n",
"acquisitionmode (MS, DIA or DDA) and\n",
"sampletype (QC, group1, group2, etc.)"), style = "color:grey"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(column(4, h5(strong("sep")),
h6(em("column delimiter."), style = "color:grey")),
column(3, textInput("sep1", "", value=","))),
fluidRow(column(4, h5(strong("dec")),
h6(em("decimal character."), style = "color:grey")),
column(3, textInput("dec1", "", value="."))),
tags$hr(style = "border-color: white"),
fluidRow(actionButton("JumpTo2", "Next >", width = "100px"),
style = "margin: 20px 0px 0px 0px")
),
mainPanel(tableOutput("metadata"))
),
tabPanel(title = "Peak-picking", value = "tab2",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
tags$head(
tags$style(HTML("input[type=\"number\"] {
height: 35px; font-size:11px
}"))),
mainPanel(
position="left",
fluidRow(column(6, h5(strong("dmzagglom (in ppm)")),
h6(em("m/z tolerance used for partitioning and clustering. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzagglom_ms1", "MS1", value = 15, min = 0, max = 100, step = 1)),
column(3, numericInput("dmzagglom_ms2", "MS2", value = 15, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtagglom (in seconds)")),
h6(em("rt window used for partitioning (in seconds). 25 by default."), style = "color:grey")),
column(3, numericInput("drtagglom_ms1", "MS1", value = 500, min = 0, max = 1000, step = 1)),
column(3, numericInput("drtagglom_ms2", "MS2", value = 500, min = 0, max = 1000, step = 1))),
fluidRow(column(6, h5(strong("drtclust (in seconds)")),
h6(em("rt window used for clustering (in seconds). 25 by default."), style = "color:grey")),
column(3, numericInput("drtclust_ms1", "MS1", value = 100, min = 0, max = 1000, step = 1)),
column(3, numericInput("drtclust_ms2", "MS2", value = 200, min = 0, max = 1000, step = 1))),
fluidRow(column(6, h5(strong("minpeak")),
h6(em("minimum number of measurements required for a peak. By default, 5 for MS1 and 4 for MS2."), style = "color:grey")),
column(3, numericInput("minpeak_ms1", "MS1", value = 5, min = 1, max = 25, step = 1)),
column(3, numericInput("minpeak_ms2", "MS2", value = 4, min = 1, max = 25, step = 1))),
fluidRow(column(6, h5(strong("minint")),
h6(em("minimum intensity of a peak. By default, 1000 for MS1 and 100 for MS2."), style = "color:grey")),
column(3, numericInput("minint_ms1", "MS1", value = 1000, min = 0, max = 1e5, step = 1)),
column(3, numericInput("minint_ms2", "MS2", value = 100, min = 0, max = 1e5, step = 1))),
fluidRow(column(6, h5(strong("drtgap (in seconds)")),
h6(em("maximum rt gap length to be filled. 5 by default."), style = "color:grey")),
column(3, numericInput("drtgap_ms1", "MS1", value = 5, min = 0, max = 30, step = 1)),
column(3, numericInput("drtgap_ms2", "MS2", value = 5, min = 0, max = 30, step = 1))),
fluidRow(column(6, h5(strong("drtminpeak (in seconds)")),
h6(em("minimum rt width of a peak. 15 by default. At least minpeak within the drtminpeak window are required to define a peak."), style = "color:grey")),
column(3, numericInput("drtminpeak_ms1", "MS1", value = 15, min = 0, max = 500, step = 1)),
column(3, numericInput("drtminpeak_ms2", "MS2", value = 15, min = 0, max = 500, step = 1))),
fluidRow(column(6, h5(strong("drtmaxpeak (in seconds)")),
h6(em("maximum rt width of a single peak. 100 by default."), style = "color:grey")),
column(3, numericInput("drtmaxpeak_ms1", "MS1", value = 100, min = 0, max = 500, step = 1)),
column(3, numericInput("drtmaxpeak_ms2", "MS2", value = 200, min = 0, max = 500, step = 1))),
fluidRow(column(6, h5(strong("maxeicpeaks")),
h6(em("maximum number of peaks within one EIC. By default, 5 for 10 and 3 for MS2."), style = "color:grey")),
column(3, numericInput("recurs_ms1", "MS1", value = 5, min = 1, max = 50, step = 1)),
column(3, numericInput("recurs_ms2", "MS2", value = 10, min = 1, max = 50, step = 1))),
fluidRow(column(6, h5(strong("weight")),
h6(em("weight for assigning measurements to a peak. By default, 2 for MS1 and 3 for MS2."), style = "color:grey")),
column(3, numericInput("weight_ms1", "MS1", value = 2, min = 1, max = 10, step = 1)),
column(3, numericInput("weight_ms2", "MS2", value = 3, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("SN")),
h6(em("signal-to-noise ratio. By default, 3 for MS1 and 2 for MS2."), style = "color:grey")),
column(3, numericInput("sn_ms1", "MS1", value = 3, min = 1, max = 10, step = 1)),
column(3, numericInput("sn_ms2", "MS2", value = 2, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("SB")),
h6(em("signal-to-base ratio. By default, 3 for MS1 and 2 for MS2."), style = "color:grey")),
column(3, numericInput("sb_ms1", "MS1", value = 3, min = 1, max = 10, step = 1)),
column(3, numericInput("sb_ms2", "MS2", value = 2, min = 1, max = 10, step = 1))),
fluidRow(column(6, h5(strong("dmzIso (in ppm)")),
h6(em("mass tolerance for isotope matching. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzIso_ms1", "MS1", value = 5, min = 0, max = 100, step = 1)),
column(3, numericInput("dmzIso_ms2", "MS2", value = 5, min = 0, max = 10, step = 1))),
fluidRow(column(6, h5(strong("drtIso")),
h6(em("rt window for isotope matching. 5 by default."), style = "color:grey")),
column(3, numericInput("drtIso_ms1", "MS1", value = 5, min = 0, max = 100, step = 1)),
column(3, numericInput("drtIso_ms2", "MS2", value = 5, min = 0, max = 100, step = 1))),
tags$hr(),
fluidRow(actionButton("GoBackTo1", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo3", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Batch processing", value = "tab3",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
tags$head(
tags$style(HTML("input[type=\"number\"] {
height: 35px; font-size:11px
}"))),
mainPanel(fluidRow(column(6, h5(strong("dmzalign")),
h6(em("mass tolerance between peak groups for alignment (in ppm). 5 by default."), style = "color:grey")),
column(3, numericInput("dmzalign", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtalign")),
h6(em("maximum rt distance between peaks for alignment (in seconds). 30 by default."), style = "color:grey")),
column(3, numericInput("drtalign", "", value = 30, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("span")),
h6(em("span parameter for loess rt smoothing. 0.4 by default."), style = "color:grey")),
column(3, numericInput("span", "", value = 0.4, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("minsamplesfracalign")),
h6(em("minimum samples fraction represented in each cluster used for alignment. 0.75 by default."), style = "color:grey")),
column(3, numericInput("minsamplesfracalign", "", value = 0.75, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("dmzgroup")),
h6(em("mass tolerance between peak groups for grouping (in ppm). 5 by default."), style = "color:grey")),
column(3, numericInput("dmzgroup", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("drtagglomgroup")),
h6(em("maximum rt distance in mz partitions for grouping (in seconds). 30 by default. It shouldn't be smaller than drtgroup."), style = "color:grey")),
column(3, numericInput("drtagglomgroup", "", value = 30, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("drtgroup")),
h6(em("maximum rt distance between peaks for grouping (in seconds). 30 by default."), style = "color:grey")),
column(3, numericInput("drtgroup", "", value = 15, min = 0, max = 200, step = 1))),
fluidRow(column(6, h5(strong("minsamplesfracgroup")),
h6(em("minimum samples fraction represented in each cluster used for grouping. 0.25 by default."), style = "color:grey")),
column(3, numericInput("minsamplesfracgroup", "", value = 0.25, min = 0, max = 1, step = 0.05))),
fluidRow(column(6, h5(strong("parallel")),
h6(em("parallelize processing. FALSE by default."), style = "color:grey")),
column(3, selectInput("parallel", "", choices = list("TRUE" = TRUE, "FALSE" = FALSE),
selected = FALSE))),
fluidRow(column(6, h5(strong("ncores")),
h6(em("number of cores to be used in case parallel is TRUE. 2 by default."), style = "color:grey")),
column(3, numericInput("ncores", "", value = 2, min = 0, max = 50, step = 1))),
tags$hr(),
fluidRow(actionButton("GoBackTo2", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo4", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Annotation", value = "tab4",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
mainPanel(fluidRow(column(6, h5(strong("dmzprecursor")),
h6(em("mass tolerance for precursor ions. 5 by default."), style = "color:grey")),
column(3, numericInput("dmzprecursor", "", value = 5, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("dmzproducts")),
h6(em("mass tolerance for product ions. 10 by default."), style = "color:grey")),
column(3, numericInput("dmzproducts", "", value = 10, min = 0, max = 100, step = 1))),
fluidRow(column(6, h5(strong("rttol")),
h6(em("total rt window for coelution between precursor and product ions. 5 by default."), style = "color:grey")),
column(3, numericInput("rttol", "", value = 5, min = 0, max = 50, step = 1))),
fluidRow(column(6, h5(strong("coelcutoff")),
h6(em("coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. 0.7 by default."), style = "color:grey")),
column(3, numericInput("coelcutoff", "", value = 0.7, min = 0, max = 1, step = 0.05))),
tags$hr(),
fluidRow(column(6, checkboxGroupInput("lipidClassesPos", "Lipid classes to annotate for ESI+ :",
c("MG" = "MG",
"LPC" = "LPC",
"LPE" = "LPE",
"PC" = "PC",
"PCo" = "PCo",
"PCp" = "PCp",
"PE" = "PE",
"PEo" = "PEo",
"PEp" = "PEp",
"PG" = "PG",
"Sphingoid bases" = "Sph",
"Sphingoid bases phosphate" = "SphP",
"Cer" = "Cer",
"AcylCer" = "AcylCer",
"CerP" = "CerP",
"SM" = "SM",
"Carnitines" = "Carnitines",
"CE" = "CE",
"DG" = "DG",
"TG" = "TG"),
selected = c("MG", "LPC", "LPE", "PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG", "Sph",
"SphP", "Cer", "AcylCer", "CerP", "SM", "Carnitines", "CE", "DG", "TG"))),
column(6, checkboxGroupInput("lipidClassesNeg", "Lipid classes to annotate for ESI+ :",
c("FA" = "FA",
"FAHFA" = "FAHFA",
"LPC" = "LPC",
"LPE" = "LPE",
"LPG" = "LPG",
"LPI" = "LPI",
"LPS" = "LPS",
"PC" = "PC",
"PCo" = "PCo",
"PCp" = "PCp",
"PE" = "PE",
"PEo" = "PEo",
"PEp" = "PEp",
"PG" = "PG",
"PI" = "PI",
"PS" = "PS",
"Sphingoid bases" = "Sph",
"Sphingoid bases phosphate" = "SphP",
"Cer" = "Cer",
"AcylCer" = "AcylCer",
"CerP" = "CerP",
"CL" = "CL",
"Bile Acids" = "BA"),
selected = c("FA", "FAHFA", "LPC", "LPE", "LPG", "LPI", "LPS",
"PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG", "PI", "PS",
"Sph", "SphP", "Cer", "AcylCer", "CerP", "CL", "BA")))),
tags$hr(),
fluidRow(actionButton("GoBackTo3", "< Previous", width = "100px",
style="margin:40px 0px"),
actionButton("JumpTo5", "Next >", width = "100px",
style="margin:40px 0px"))
)),
tabPanel(title = "Run", value = "tab5",
h4("LipidMS: Lipid annotation for LC-MS/MS data"),
tags$hr(),
sidebarPanel(width = 3,
fluidRow(h5("\nRun your job: "),
style = "margin: 20px 0px 0px 0px"),
fluidRow(actionButton("do", "Run",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
tags$hr(style = "border-color: white"),
fluidRow(h5("\nDownload your results: "),
h6(em("(Wait until your results show up on the main panel)")),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadSummary", "Summary Tables",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadPeaklist", "Annotated Peaklists",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadBatchResults", "Batch Results (if applied)",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
fluidRow(downloadButton("downloadPlots", "Plots",
style="color: #fff; background-color: #669999; border-color: #000"),
style = "margin: 20px 0px 0px 0px"),
tags$hr(style = "border-color: white"),
fluidRow(actionButton("GoBackTo4", "< Previous", width = "100px",
style="margin:40px 0px"),
style = "margin: 20px 0px 0px 0px")
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel("Summary Tables Annotation", tableOutput("summaryTable")),
tabPanel("Annotated Peaklists", tableOutput("annotatedPeaklist")),
tabPanel("Batch Results", tableOutput("features"))
)
))
)
)
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