R/plotTracesResids.R

In glotaran/TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"plotTracesResids" <- function(multimodel, multitheta, plotoptions) {
  oldpar <- par(no.readonly = TRUE)
  on.exit(par(oldpar))
  if (dev.cur() != 1) {
    dev.new()
  }
  m <- multimodel@modellist
  t <- multitheta
  res <- multimodel@fit@resultlist
  superimpose <- plotoptions@superimpose
  if (length(superimpose) < 1 || any(superimpose > length(m))) {
    superimpose <- 1:length(m)
  }
  allx2 <- allx <- vector()
  for (i in superimpose) {
    allx2 <- append(allx2, m[[i]]@x2)
    allx <- append(allx, m[[i]]@x)
  }
  if (length(plotoptions@xlim) == 0) {
    xmax <- max(allx)
    xmin <- min(allx)
  }
  allx2 <- sort(unique(allx2))
  ## set up plot layout
  par(plotoptions@paropt)
  par(mgp = c(2, 1, 0), mar = c(0, 2, 3, 0), oma = c(1, 0, 4, 0))
  if (length(plotoptions@selectedtraces) > 0) {
    seltraces <- plotoptions@selectedtraces
    xx <- vector()
    for (i in superimpose) {
      xx <- append(m[[i]]@x2[seltraces], xx)
    }
    lensel <- length(unique(xx))
  } else {
    seltraces <- 1:length(allx2)
    lensel <- length(seltraces)
  }
  resList <- vector("list", length = length(m))
  maxr <- vector(length = length(m))
  for (i in 1:length(m)) {
    resList[[i]] <- as.matrix(unlist(res[[i]]@resid),
      byrow = (m[[i]]@clpType == "x")
    )
    dim(resList[[i]]) <- dim(m[[i]]@psi.df)
  }
  xx <- do.call(rbind, resList)
  ymin <- apply(xx, 2, min)
  ymax <- apply(xx, 2, max)
  par(mfrow = n2mfrow(lensel))
  for (j in 1:length(allx2)) {
    plotted <- FALSE
    for (i in 1:length(m)) {
      k <- which(m[[i]]@x2 == allx2[j])[1]
      if (i %in% superimpose && k %in% seltraces) {
        irfmu <- res[[i]]@irfvec[[k]][1]
        rr <- resList[[i]][, k]
        if (!plotted) {
          linlogplot(m[[i]]@x, rr, irfmu,
            plotoptions@linrange,
            type = "l",
            ylim = c(ymin[j], ymax[j]), xlim = c(xmin, xmax),
            xlab = plotoptions@xlab, lty = 1,
            ylab = "amplitude", col = i
          )
          title(signif(m[[i]]@x2[k]), line = 0)
          plotted <- TRUE
        } else {
          lines(linloglines(m[[i]]@x, irfmu, plotoptions@linrange),
            rr,
            col = i, type = "l", lty = 1
          )
        }
      }
    }
  }
  if (length(plotoptions@title) != 0) {
    tit <- plotoptions@title
    if (plotoptions@addfilename) tit <- paste(tit, m[[i]]@datafile)
  } else {
    tit <- ""
    if (plotoptions@addfilename) {
      tit <- paste(tit, m[[i]]@datafile)
    }
  }
  mtext(tit, side = 3, outer = TRUE, line = 1)
  par(las = 2)
  ## MAKE PS
  if (dev.interactive() && length(plotoptions@makeps) != 0) {
    if (plotoptions@output == "pdf") {
      pdev <- pdf
    } else {
      pdev <- postscript
    }
    dev.print(
      device = pdev,
      file = paste(plotoptions@makeps, "_tracesresids.",
        plotoptions@output,
        sep = ""
      )
    )
  }
}