R/global.R

In tkimhofer/msbrowser: Viz tool for xcms peak picking parameter optimisation

#' @importFrom shinyWidgets numericRangeInput radioGroupButtons
#' @import shiny
#' @importFrom shinycssloaders withSpinner
#' @importFrom shinybusy add_busy_bar
#' @importFrom shinyBS bsTooltip

globalVariables(c("peak"))
#
# lib_file=system.file(file.path("inst", "extdata", "signalDB.csv", fsep = .Platform$file.sep), package = "msbrowser")
# icst <- read.table(lib_file,
#     sep = ",", stringsAsFactors = FALSE, comment.char = "#", blank.lines.skip = TRUE,
#     row.names = NULL, skip = 1, col.names = c("assay", "compound", "mz",
#         "rt", "info"))
# icst <- icst[icst$assay != "" & !is.na(icst$assay), ]
#
#save(icst, file = 'inst/extdata/icst.rda')

load('inst/extdata/icst.rda')

ui_par_centwave <- fluidRow(column(12, offset = 0.2, h4("Parameterisation"),
    helpText("The following peak picking parameters values are xcms pre-adjusted - these nearly always require optimisation for each instrumental setup.")),
    hr(), column(4, numericInput(inputId = "in_mzdev", label = paste0("ppm"),
        value = 15), bsTooltip("in_mzdev", "Maximal tolerated m/z deviation in consecutive scans in parts per million (ppm)"),
        br(), sliderInput("in_rtrange", "peakwidth (s)", min = 2, max = 100,
            step = 1, value = c(20, 50)), bsTooltip("in_rtrange", "Expected chromatographic peak width (elution/scan time). Given as range (min, max) in seconds"),
        br(), numericInput("in_mzdiff", label = "mzdiff", value = 0.1),
        bsTooltip("in_mzdiff", "Minimum closeness in m/z dimension for peaks with overlapping retention times; can take negative values, indicating a single data point can be allocated to two different features.")),
    column(4, numericInput(inputId = "in_noise", label = "noise", value = 100),
        br(), numericInput(inputId = "in_sn", label = "snthresh", value = 10),
        br(), selectInput("in_mzCentFun", label = "mzCenterFun", choices = c(`Weighted Mean` = "wMean",
            Mean = "mean", `Peak apex` = "apex", `Weighted mean of peak apex and neigbouring scans` = "wMeanApex3",
            `Mean of peak apex and neigbouring scans` = "meanApex3"))),
    column(4, wellPanel(h5("prefilter"), numericInput("in_prefilter_k",
        label = "Number of consecutive scans...", min = 3, max = 10, value = 3),
        br(), numericInput("in_prefilter_I", label = "...exceeding Intensity of",
            min = 3, max = 10, value = 3)), br(), selectInput("in_integrate",
        label = "integrate", choices = c(`Descend Mexican Hat` = "1", `MS data` = "2"),
        selected = "1"), checkboxInput("in_fitgauss", label = "fitgauss",
        value = FALSE)))

ui_par_matchedFilter <- fluidRow(h4("Parameterisation"), helpText("Specify the expected mass to charge ratio (m/s) and retention time in seconds (s) of a compound. Use the list below to select pre-defined internal chemical standards (ICS) for HILIC positive ionisation mode (v+)."),
    hr(), column(4, numericInput(inputId = "in_fwhm", label = paste0("FWHM of matched filtration Gaussian"),
        value = 30), br(), numericInput("in_sigma", "SD of matched Gaussian",
        value = 2.3548)), column(4, numericInput(inputId = "in_step", label = "Bin width m/z dim.",
        value = 0.1), br(), numericInput(inputId = "in_steps", label = "Bin to merge before filtration",
        value = 2), br(), numericInput(inputId = "in_mzdiff", label = "Min. difference mz for peaks w overlapping rt's",
        value = 0.8)), column(4, numericInput("in_max", label = "Maximum  number expected peaks / slice",
        value = 5), br(), numericInput(inputId = "in_snthres", label = "S/N cutoff chromatogr. dim.",
        value = 100)))

uiT_ichron <- tabPanel("Chromatograms and mass spectrum", value = "ichron",
    br(), withSpinner(plotlyOutput("tic_bpc"), type = 8), withSpinner(plotlyOutput("xic"),
        type = 8), withSpinner(plotlyOutput("ssms"), type = 8), add_busy_bar(color = "#FBDD00"))

uiT_rawData <- tabPanel(title = "Raw Data", value = "rawData", fluidRow(style = "height:1040px;",
    withSpinner(plotlyOutput("rawdd", width = "100%", inline = TRUE), type = 4,
        color = "#0dc5c1")), add_busy_bar(color = "#FBDD00"))

uiT_ppick <- tabPanel("Detected Features", value = "ppick", fluidRow(style = "height:1040px;",
    withSpinner(plotlyOutput("pp1", width = "100%", inline = TRUE), type = 4)),
    fluidRow(column(width = 11, wellPanel(span(h4("R console commands"),
        style = "color: black"), span(textOutput("Rcode_loadp"), style = "font-family: Courier,courier; font-size:100%"),
        br(), span(textOutput("Rcode_file"), style = "font-family: Courier,courier; font-size:100%"),
        span(textOutput("Rcode_readIn"), style = "font-family: Courier,courier; font-size:100%"),
        br(), span(textOutput("Rcode_ppick"), style = "font-family: Courier,courier; font-size:100%"))),
        add_busy_bar(color = "#FBDD00")))

uiT_peaks <- tabPanel("Feature Table", value = "peaks", column(8, align = "center",
    br(), fluidRow(DT::DTOutput("PeakTbl", width = "auto", height = "auto")),
    br(), fluidRow(actionButton(inputId = "plotselection", "Plot Peak Intensities"))),
    column(4, align = "center", plotlyOutput("peakplt", width = "80%",
        height = "auto", inline = FALSE), plotlyOutput("peakpltIso", width = "80%",
        height = "auto", inline = FALSE)), add_busy_bar(color = "#FBDD00"))

uiE_div_xic <- div(id = "div_xic", fluidRow(column(8, numericRangeInput(inputId = "xic_ra",
    label = NA, value = c(200, 201), separator = " to ", width = "100%")),
    column(2, actionButton("go_xic", "Go"))))

uiE_div_summary_file <- div(id = "summary_file", column(12, offset = -1,
    align = "center", br(), textOutput("msfile"), br(), tableOutput("datsum")),
    br(), column(12, offset = 0.7, align = "left", checkboxInput("imp_xic",
        "Select m/z range for XIC manually", value = FALSE)), br(), div(id = "proceed",
        br(), br(), column(12, offset = 0.7, align = "center", p(tags$strong(HTML("<span style=\"color:#33A2FF\">Click on signal in mass spectrum to proceed!</span>"))))))

uiE_div_inp_col <- div(id = "div_input_collapse", fluidRow(column(12, offset = 0.7,
    fluidRow(column(10, actionButton("filechoose", label = "Select file"),
        textOutput("bname", inline = TRUE), actionButton("fileexample",
            label = "Load Example", inline = TRUE), bsTooltip(id = "filechoose",
            title = "Choose an LC-MS data file in open data format (e.g., mzML)",
            placement = "right", options = list(container = "body")), bsTooltip(id = "fileexample",
            title = "Use an example LC-MS file.", placement = "right",
            options = list(container = "body")))), br(), uiOutput("ss1"),
    add_busy_bar(color = "#FBDD00"))))

uiE_move <- fluidRow(column(12, align = "right", actionButton("move", "Let's move on!",
    icon("thumbs-up"), style = "color: #fff; background-color: #33A2FF; border-color: #33A2FF")))

uiE_target <- div(id = "div_target", h3(a(href = "#", onclick = "doThat(this)",
    "2. Select target signal")), helpText("Specify a spectral area either through clicking in mass spectrum or by manual entry of a scantime and m/z value. Alternatively, select a compound listed in a database table."),
    br())

uiE_div_tar_col <- div(id = "target_col", div(id = "selectors", column(12,
    offset = 0.7, align = "center", radioButtons("target_input", label = NULL,
        choices = c(`Cursor selection` = "click", Manual = "man", Database = "db"),
        inline = TRUE, selected = "click"), conditionalPanel("input.target_input=='click'",
        helpText("The chromatograms in the main panel can be used to identify target areas of high and low signal intensity."),
        br(), textOutput("selection"), ), )), column(12, offset = 0.7,
    conditionalPanel("input.target_input=='man'", helpText("Enter spectral region manually"),
        br(), fluidRow(column(12, column(width = 8, numericInput(inputId = "in_rt",
            "Retention time (s)", value = 98.4)), column(width = 4, numericInput(inputId = "in_rt_ws",
            "window size (s)", value = 25)))), fluidRow(column(12, column(width = 8,
            numericInput(inputId = "in_mz", "Mass to charge ratio", value = 269.1109)),
            column(width = 4, numericInput(inputId = "in_mz_ws", "window size",
                value = 10))))), conditionalPanel("input.target_input=='db'",
        helpText("Compund values below are instrument and assay specific!",
            tags$strong("Interprete carefully, since scan times vary!"),
            "Please refer to the ", a("GitHub Wiki", href = "https://github.com/tkimhofer/msbrowser/wiki/Database-Table-Editing",
                target = "_blank"), "for instructions on database personalisation."),
        br(), fluidRow(column(4, radioGroupButtons(inputId = "db_assays",
            label = "Assay type", choices = unique(as.character(icst$assay)),
            direction = "horizontal")), column(8, selectizeInput("in_icst",
            label = "Compounds", choices = c("Select assay")), textOutput("compound_info"),
            br())), br()), br()), fluidRow(column(12, align = "right",
    br(), actionButton("move_picks", "Generate plot", icon("thumbs-up"),
        style = "color: #fff; background-color: #33A2FF; border-color: #33A2FF"))),
    fluidRow(div(id = "selectors1", column(12, offset = 0.7, align = "left",
        checkboxInput("imp_vis", "Viz options", value = FALSE)))))

uiE_div_ppick <- div(id = "div_ppick", h3("3. Perform peak picking"), helpText("Select peak picking algorighm from the list below"),
    fluidRow(align = "center", offset = 0.7, column(12, offset = 0.7, br(),
        fluidRow(align = "center", selectInput("in_pickMethod", label = "Algorithm",
            choices = c(CentWave = "centWave", `Matched Filter` = "matchedFilter"))),
        conditionalPanel(condition = "input.in_pickMethod=='centWave'",
            fluidRow(h4("Parameters"), helpText("The following peak picking parameters are the standard parameters defined by xcms - these nearly always require optimisation for each data set (most importantly: ppm, rt range and noise level)."),
                hr(), column(4, numericInput(inputId = "in_mzdev", label = paste0("m/z deviation [ppm]"),
                value = 25), br(), sliderInput("in_rtrange", "Elution time range (s) [peakwidth]",
                min = 1, max = 100, step = 1, value = c(20, 50)), br(),
                numericInput("in_mzdiff", label = "Minimum diff m/z overlap [mzdiff]",
                value = -0.001), br(), fluidRow(h4(a("Need parameter help?",
                href = "https://tkimhofer.github.io/msbrowser/articles/pars.html",
                target = "_blank")))), column(4, numericInput(inputId = "in_noise",
                label = "Noise", value = 0), br(), numericInput(inputId = "in_sn",
                label = "Signal/Noise threshold [snthresh]", value = 10),
                br(), selectInput("in_mzCentFun", label = "m/z center function",
                choices = c(`Weighted Mean` = "wMean", Mean = "mean",
                `Peak apex` = "apex", `Weighted mean of peak apex and neigbouring scans` = "wMeanApex3",
                `Mean of peak apex and neigbouring scans` = "meanApex3")),
                br(), selectInput("in_integrate", label = "Integration method [integrate]",
                choices = c(`1: Mexican Hat` = "1", `2: Real MS data` = "2"),
                selected = "1")), column(4, wellPanel(h5("Pre-filter"),
                numericInput("in_prefilter_k", label = "Number of scans [k]",
                min = 0, max = 100, value = 3), br(), numericInput("in_prefilter_I",
                label = "Intensity [I]", min = 0, max = 1e+07, value = 100)),
                br(), checkboxInput("in_fitgauss", label = "Fit Gaussian to each peak [fitgauss]",
                value = FALSE)))), conditionalPanel(condition = "input.in_pickMethod=='matchedFilter'",
            fluidRow(h4("Parameters"), helpText("The following peak picking parameters are the standard parameters defined by xcms - these nearly always require optimisation for each data set."),
                hr(), column(4, numericInput(inputId = "in_fwhm", label = paste0("FWHM of matched filtration Gaussian"),
                  value = 30), br(), numericInput("in_sigma", "SD of matched Gaussian",
                  value = 2.3548)), column(4, numericInput(inputId = "in_step",
                  label = "Bin width m/z dim.", value = 0.1), br(), numericInput(inputId = "in_steps",
                  label = "Bin to merge before filtration", value = 2),
                  br(), numericInput(inputId = "in_mzdiff", label = "Min. difference mz for peaks w overlapping rt's",
                    value = 0.8)), column(4, numericInput("in_max", label = "Maximum  number expected peaks / slice",
                  value = 5), br(), numericInput(inputId = "in_snthres",
                  label = "S/N cutoff chromatogr. dim.", value = 100)))),
        conditionalPanel(condition = "input.in_pickMethod=='dbscan'", fluidRow(h4("Parameters"),
            helpText("The following are pre-defined paramter values, these should be tested for every data set."),
            hr(), column(4, numericInput(inputId = "in_ppm", label = paste0("inflate mz to accommodate detectors m/z accuracy (ppm in xcms)"),
                value = 10000), numericInput(inputId = "in_ppm_mztrans",
                label = paste0("transformation factor to match rt stepsize"),
                value = 15)), column(4, numericInput(inputId = "in_eps",
                label = "Radius of neighbourhood", value = 1), br(), numericInput("in_minPts",
                "Minimum Number of points in each neighbourhood", value = 2)),
            column(4, numericInput(inputId = "in_noise", label = paste0("noise threshold"),
                value = 1), br(), numericInput(inputId = "in_rttrans",
                label = paste0("rt trans (might not be needed)"), value = 1)))))),
    actionButton("pickpeak1", label = "Pick Peaks!", icon("thumbs-up"),
        style = "color: #fff; background-color: #33A2FF; border-color: #33A2FF"))

xic_mzrange <- function(xic_mz, ppm) {

    mz_window <- (xic_mz * (ppm/10^6))/2
    low <- xic_mz - mz_window
    high <- xic_mz + mz_window
    return(c(xic_mz - mz_window, xic_mz + mz_window, xic_mz))

}