In yufree/mzrtsim: Raw data (mzML) and peaks list simulation for LC/GC-MS based metabolomics data

knitr::opts_chunk$set(echo = F)
library(shiny)
library(DT)
library(mzrtsim)
data("hmdbcms")
data("monams1")
data("monahrms1")

Input data

inputPanel(
        sliderInput(
        "n",
        "Numbers of the compounds",
        min = 10,
        max = 500,
        step = 1,
        value = 100
        ),
        sliderInput(
        "inscutoff",
        "intensity cutoff for MS1 spectra",
        min = 0,
        max = 0.5,
        step = 0.01,
        value = 0.05
        ),
        sliderInput(
        "ppm",
        "mass to charge ratio shift in ppm",
        min = 0,
        max = 50,
        value = 5
        ),
        sliderInput(
        "sampleppm",
        "m/z shift in ppm within one sample",
        min = 0,
        max = 50,
        value = 5
        ),
        sliderInput(
        "mzrange",
        "mass to charge ratio range",
        min = 50,
        max = 1500,
        value = c(100,1000)
        ),
        sliderInput(
        "rtrange",
        "retention time range",
        min = 0,
        max = 1000,
        value = c(0,600)
        ),
        sliderInput(
        "scanrate",
        "scan rate per secound",
        min = 0,
        max = 1,
        value = 0.2
        ),
        textInput("pwidth", "peak width for all peaks", value = "10"),
        textInput("pheight", "peak height for all peaks", value = "12,9,16,13,10,9,5,11,7,11,13,9,7,18,11,12,9,15,10,13,16,13,10,9,5,11,7,11,13,9,9,15,10,13,16,13,10,9,5,11,13,9,7,18,11,12,9,15,10,13,12,9,16,13,10,9,5,11,7,11,13,9,7,18,11,12,9,15,10,13,16,13,10,9,5,11,7,11,13,9,9,15,10,13,16,13,10,9,5,11,13,9,7,18,11,12,9,15,10,13"),
        sliderInput(
        "baseline",
        "noise baseline",
        min = 50,
        max = 1000,
        value = 100
        ),
        sliderInput(
        "baselinesd",
        "standard deviation for noise",
        min = 0,
        max = 100,
        value = 30
        ),
        textInput("rf", "response factor of all compounds", value = "100"),
        sliderInput(
        "tailingfactor",
        "tailing factor for peaks",
        min = 0.5,
        max = 2,
        value = 1.2
        ),
        textInput("name", "Enter File Name:", value = "test"),
        numericInput("seed", "Enter Seed:", value = 1),
        radioButtons(inputId = 'db', label='database', choices = c('HMDB','MoNA','MoNAhr'), selected = 'MoNAhr'),
        checkboxInput('unique','Unique compound name',value = TRUE)
        )
sim <- reactive({
        if(input$db == 'HMDB'){
                data("hmdbcms")
                simmzml(
                        name=input$name,
                        db=hmdbcms,
                        n = input$n,
                        inscutoff = input$inscutoff,
                        mzrange = input$mzrange,
                        rtrange = input$rtrange,
                        ppm = input$ppm,
                        sampleppm = input$sampleppm,
                        scanrate = input$scanrate,
                        pwidth = as.numeric(input$pwidth),
                        pheight = as.numeric(trimws(unlist(strsplit(input$pheight, ",")))),
                        baseline = input$baseline,
                        baselinesd = input$baselinesd,
                        rf = as.numeric(input$rf),
                        tailingfactor = input$tailingfactor,
                        seed=input$seed,
                        unique=input$unique
                 )
                file1 <- paste0(input$name,'.mzML')
                file2 <- paste0(input$name,'.csv')
                return(list(file1 = file1, file2 = file2))
        } else if(input$db == 'MoNA'){
                data("monams1")
                simmzml(
                        name=input$name,
                        db=monams1,
                        n = input$n,
                        inscutoff = input$inscutoff,
                        mzrange = input$mzrange,
                        rtrange = input$rtrange,
                        ppm = input$ppm,
                        sampleppm = input$sampleppm,
                        scanrate = input$scanrate,
                        pwidth = as.numeric(input$pwidth),
                        pheight = as.numeric(trimws(unlist(strsplit(input$pheight, ",")))),
                        baseline = input$baseline,
                        baselinesd = input$baselinesd,
                        rf = as.numeric(input$rf),
                        tailingfactor = input$tailingfactor,
                        seed=input$seed,
                        unique=input$unique
                 )
                file1 <- paste0(input$name,'.mzML')
                file2 <- paste0(input$name,'.csv')
                return(list(file1 = file1, file2 = file2))
        }else{
                data("monahrms1")
                simmzml(
                        name=input$name,
                        db=monahrms1,
                        n = input$n,
                        inscutoff = input$inscutoff,
                        mzrange = input$mzrange,
                        rtrange = input$rtrange,
                        ppm = input$ppm,
                        sampleppm = input$sampleppm,
                        scanrate = input$scanrate,
                        pwidth = as.numeric(input$pwidth),
                        pheight = as.numeric(trimws(unlist(strsplit(input$pheight, ",")))),
                        baseline = input$baseline,
                        baselinesd = input$baselinesd,
                        rf = as.numeric(input$rf),
                        tailingfactor = input$tailingfactor,
                        seed=input$seed,
                        unique=input$unique
                 )
                file1 <- paste0(input$name,'.mzML')
                file2 <- paste0(input$name,'.csv')
                return(list(file1 = file1, file2 = file2))
        }
})

Simulated data

Simulated data

shiny::renderPlot({
        sim <- suppressWarnings(sim())
        x <- mzmlviz(sim$file1)
})

Simulated data table

DT::renderDataTable({
                sim <- suppressWarnings(sim())
                read.csv(sim$file2)
        })

Download data

Raw data

downloadHandler(
        filename = paste0(input$name,'.mzML'),
        content = function(file) {
      files <- sim()
      file.copy(files$file1, file)
    }
)

Peaks list csv data

downloadHandler(
        filename = paste0(input$name,'.csv'),
        content = function(file) {
      files <- sim()
      file.copy(files$file2, file)
    }
)

yufree/mzrtsim documentation built on Feb. 18, 2025, 6:29 a.m.