In nathaniel-mahieu/centWaveP: CWT Based Chromatographic Peak Detection

library(xcms)
library(ggplot2)
library(gridExtra)
devtools::load_all("C:/Dropbox/GitHub/centWaveP")

xr = xcmsRaw("../../../Projects/Datasets/2nm118a_nh2_negative_ecoli_1213/2NM118A_HILICAnnoWgN14_2NM111G_12.mzXML")

roi.l = cent(xr, ppm = 2, prefilter = c(4,0), maxskip = 5) # ppm is added to both sides
eic.l = lapply(sample(roi.l, 3000), roiToEic, xr, padding=100))
eic.noise.l = lapply(eic.l, estimateBaselineNoise, peakwidth = c(15, 60), minslope.peak = 20000)

peaks = lapply(seq_along(eic.noise.l), function(i) {
  cat(i, "\r       ")
  wave(eic.noise.l[[i]], peakwidth = c(15, 70), valleywidth.min = 15, sensitivity = 1, smooth = T)
})



index = lapply(seq(peaks), function(i) {
  wns = peaks[[i]]$descent.fold.above.descentbaseline

  cbind(roi = rep(i, length(wns)), wsn = wns, num = seq_along(wns))

  }) %>% do.call(what = rbind)


ps0 = lapply(sample(which(index[,"wsn"] < 1), 16, replace = T), function(x) {
  plotWavePeak(unname(index[x, "num"]), eic.noise.l[[index[x,"roi"]]], peaks[[index[x,"roi"]]])
})

ps1 = lapply(sample(index[,"wsn"] %>% { which(. > 1  & . < 2) }, 16, replace = T), function(x) {
  plotWavePeak(unname(index[x, "num"]), eic.noise.l[[index[x,"roi"]]], peaks[[index[x,"roi"]]])
})

ps2 = lapply(sample(index[,"wsn"] %>% { which(. > 2  & . < 3) }, 16, replace = T), function(x) {
  plotWavePeak(unname(index[x, "num"]), eic.noise.l[[index[x,"roi"]]], peaks[[index[x,"roi"]]])
})

ps3 = lapply(sample(index[,"wsn"] %>% { which(. > 3  & . < 5) }, 16, replace = T), function(x) {
  plotWavePeak(unname(index[x, "num"]), eic.noise.l[[index[x,"roi"]]], peaks[[index[x,"roi"]]])
})

ps4 = lapply(sample(index[,"wsn"] %>% { which(. > 5) }, 16, replace=T), function(x) {
  plotWavePeak(unname(index[x, "num"]), eic.noise.l[[index[x,"roi"]]], peaks[[index[x,"roi"]]])
})


do.call(grid.arrange, ps0)  
do.call(grid.arrange, ps1)  
do.call(grid.arrange, ps2)
do.call(grid.arrange, ps3)
do.call(grid.arrange, ps4)


which(!sapply(peaks, is.null))
i = 99
plotWavePeak(1, eic.noise.l[[i]], peaks[[i]])
peaks[[i]]
i = i+1