Example of extracted ion chromatograms

extracted_ion_chromatograms.R

library(ggplot2)
library(mzR)

mass <- c( 654.3920, 668.3920)

numCores <- parallel::detectCores()
numCores <- ifelse(numCores > 2,
                   numCores - 1,
                   1)

cl <- parallel::makeCluster(numCores)

abc <-  parallel::parLapply(cl, 
                            mass, 
                            function(mass){
                              tol <- .05
                              base_dir <- "C:/Users/chase/Documents/GitHub/labNotebook"
                              mzml <- list.files(file.path(base_dir, 
                                                           "data/untargeted_sponge_discovery/p114/crude_xad16_extract/qtof/mzml_centroid_vendor"),
                                                 pattern = "mzML",
                                                 full.names = T)
                              mzml <- mzml[3:5]
                              spec <- lapply(mzml, mzR::openMSfile)
                              names(spec) <- sapply(basename(mzml), function(x) strsplit(x, "_")[[1]][[1]])
                              lapply(spec,
                                     function(x){
                                       
                                       pp <- mzR::header(x)
                                       ms1 <- pp$msLevel == 1
                                       ret <- pp$retentionTime[ms1]
                                       scans <- mzR::spectra(x)[ms1]
                                       int <- sapply(scans, function(x) {
                                         a <- x[,1] < mass + tol
                                         b <- x[,1] > mass - tol
                                         sum(x[which(a+b == 2),2])
                                       })
                                       
                                       return(data.frame(ret = ret, 
                                                         int = int,
                                                         mass = mass))
                                     })
                            })
parallel::stopCluster(cl)

abc2 <- lapply(abc, 
               function(a){
                 a1 <- lapply(a, cbind.data.frame)
                 a1 <- lapply(seq_along(a1), function(x) cbind.data.frame(a1[[x]], facet = names(a1)[[x]]))
                 do.call(rbind.data.frame, a1)
               })

abc3 <- do.call(rbind.data.frame, abc2)


cbPalette <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

ggplot(data = abc3) + 
  geom_line(aes(x = ret, 
                y = int,
                col = factor(mass)),
            size = 1) + 
  scale_colour_manual(values = cbPalette,
                      name = bquote(italic("m/z"))) + 
  scale_x_continuous(expand = c(0,0))+
  scale_y_continuous(labels = function(x) format(x, scientific = TRUE, digits = 1),
                     breaks = function(x) c(0, max(x)/2 , max(x))) + 
  xlab("Retention (s)") + 
  ylab("Intensity") + 
  facet_wrap(~facet,
             ncol = 1, 
             scale = "free_y") + 
  ggtitle("Extracted Ion Chromatograms")