LipidMS (version 3.0.0)

plotLipids: Plot informative peaks for lipid annotation

Description

Plot informative peaks for each lipid annotated with idPOS and idNEG (or similar functions).

Usage

plotLipids(msobject, span = 0.4, ppm = 10)

Arguments

msobject

annotated msobject.

span

smoothing parameter. Numeric value between 0 and 1.

ppm

mz tolerance for EIC. If set to 0, the EIC will not be shown.

Value

msobject with a plots element which contains a list of plots. Plots on the left side represent raw values while plots on the left are smoothed or clean scans (MS2 in DDA).

Details

Peak intensities are relative to the maximum intensity of each peak to ease visualization.

Grey lines show the the extracted ion chromatograms for the peaks.

Examples

# NOT RUN {
devtools::install_github("maialba3/LipidMSdata2")

library(LipidMS)

# for msobjects
#####################
msobject <- idPOS(msobject)
msobject <- plotLipids(msobject)

# display the first plot
msobject$annotation$plots[[1]]
msobject$annotation$plots[["yourpeakIDofinterest"]]

# save plots to a pdf file
pdf("plotresults.pdf")
for (p in 1:length(msobject$annotation$plots)){
  print(msobject$annotation$plots[[p]])
}
dev.off()



# for msobjects
#####################
msbatch <- annotatemsbatch(msbatch)

# lipids plots
for (m in 1:length(msbatch$msobjects)){
  if (msbatch$msobjects[[m]]$metaData$generalMetadata$acquisitionmode %in% c("DIA", "DDA")){
    msbatch$msobjects[[m]] <- plotLipids(msbatch$msobjects[[m]])
  }
}

# save plots to a pdf file
for (s in 1:length(msbatch$msobjects)){
  if (msbatch$msobjects[[s]]$metaData$generalMetadata$acquisitionmode %in% c("DIA", "DDA")){
    print(s)
    if (msbatch$msobjects[[s]]$metaData$generalMetadata$acquisitionmode == "DIA"){
      height <- 7
    } else {
      height <- 9
    }
    pdf(file = gsub(".mzXML", "_plots.pdf", msbatch$msobjects[[s]]$metaData$generalMetadata$file), 
        width = 8, height = height)
    for ( pl in 1:length(msbatch$msobjects[[s]]$annotation$plots)){
      print(msbatch$msobjects[[s]]$annotation$plots[[pl]])
    }
    dev.off()
  }
}

# }
# NOT RUN {
# }