R baseline package saving plots in a loop

Question

I'm trying to optimize the parameters for baseline in the R baseline package by changing each parameters in a loop and comparing plots to determine which parameters give me the best baseline. I currently have the code written so that the loop produces each plot, but I'm having trouble with getting the plot saved as the class of each object I'm creating is a baseline package-specific (which I'm suspecting is the problem here).

foo <- data.frame(Date=seq.Date(as.Date("1957-01-01"), by = "day", 
                        length.out = ncol(milk$spectra)),
          Visits=milk$spectra[1,],
          Old_baseline_visits=milk$spectra[1,], row.names = NULL)
foo.t <- t(foo$Visits)
#the lines above were copied from https://stackoverflow.com/questions/37346967/r-packagebaseline-application-to-sample-dataset to make a reproducible dataset

df <- expand.grid(lambda=seq(1,10,1), p=seq(0.01,0.1,0.01))
baselinediff <- list()

for(i in 1:nrow(df)){
  thislambda <- df[i,]$lambda
  thisp <- df[i,]$p
  thisplot <- baseline(foo.t, lambda=thislambda, p=thisp, maxit=20, method='als')
  print(paste0("lambda = ", thislambda))
  print(paste0("p = ", thisp))
  print(paste0("index = ", i))
  baselinediff[[i]] <- plot(thisplot)
  jpeg(file = paste(baselinediff[[i]], '.jpeg', sep = ''))
  dev.off()
}

I know that I would be able to extract corrected spectra using baseline.als but I just want to save the plot images with the red baseline so that I can see how well the baselines are getting drawn. Any baseline users out there that can help?

Ben Nutzer · Accepted Answer · 2019-06-06T06:26:20.377

I suggest you change your loop in the following way:

for(i in 1:nrow(df)){
  thislambda <- df[i,]$lambda
  thisp <- df[i,]$p
  thisplot <- baseline(foo.t, lambda=thislambda, p=thisp, maxit=20, method='als')
  print(paste0("lambda = ", thislambda))
  print(paste0("p = ", thisp))
  print(paste0("index = ", i))
  baselinediff[[i]] <- thisplot
  jpeg(file = paste('baseline', i, '.jpeg', sep = ''))
  plot(baselinediff[[i]])
  dev.off()
}

Note that this does not try to capture the already plotted element (thisplot) inside of the list. Instead, the plotting is done after you call the jpeg command. This solves your export issue. Another problem was the naming of the file. If you call baselinediff[[i]] inside of paste, you apparently end up with an error. So I switched it to a simpler name. To plot your resulting list, call:

lapply(baselinediff, plot)

If you are determined on storing the already plotted element, the capture.plotfunction from the imager package might be a good start.

This is exactly what I was trying to do, thank you so much! – Jennifer Jun 06 '19 at 16:40 — Jennifer, Jun 06 '19 at 16:40

R baseline package saving plots in a loop

1 Answers1