Working state, but not backwards compatible

In this commit, the separatation of plots for observed variables works.
The formatting should be improved.

However, in gmkin, plotting with show_residuals = TRUE is used, and the
GUI expects that the residual plot is below the main plot. This
behaviour should be restored.

5 files changed, 134 insertions, 69 deletions

diff --git a/NEWS.md b/NEWS.md
index 6669fdb2..c4b74b4a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,6 +6,10 @@
 
 - The title was changed to `Kinetic evaluations of chemical degradation data`
 
+- `plot.mkinfit`: If a residual plot is requested, show it next to the plot of the fit, not below. This may cause existing code to produce bad-looking plots, but was done to make the next feature possible without increasing code complexity too much.
+
+- `plot.mkinfit`: Add the possibility to show fits and residual plots separately for the observed variables
+
 - The main vignette `mkin` was converted to R markdown and updated
 
 - The function `add_err` was added to the package, making it easy to generate simulated data using an error model based on the normal distribution
@@ -26,7 +30,9 @@
 
 - `mkinfit`: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.
 
-- `plot.mmkin`: Removed some leftover code that set the plot margins wrongly in the case of a single fit to be plotted, so the main title was misplaced
+- `plot.mmkin`: Removed some leftover code that set the plot margins wrongly in the case of a single fit to be plotted, so the main title was misplaced.
+
+- `plot.mkinfit`: Correct default values for `col_obs`, `pch_obs` and `lty_obs` for the case that `obs_vars` is specified.
 
 ## mkin 0.9.42 (2016-03-25)
 
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 6ca7e531..6bc64351 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2015 Johannes Ranke
+# Copyright (C) 2010-2016 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -22,18 +22,16 @@ plot.mkinfit <- function(x, fit = x,
   xlab = "Time", ylab = "Observed",
   xlim = range(fit$data$time), 
   ylim = "default",
-  col_obs = 1:length(fit$mkinmod$map),
+  col_obs = 1:length(obs_vars),
   pch_obs = col_obs, 
-  lty_obs = rep(1, length(fit$mkinmod$map)),
+  lty_obs = rep(1, length(obs_vars)),
   add = FALSE, legend = !add, 
   show_residuals = FALSE, maxabs = "auto",
+  sep_obs = FALSE, rel.height.middle = 0.9,
   lpos = "topright", inset = c(0.05, 0.05), ...)
 {
   if (add && show_residuals) stop("If adding to an existing plot we can not show residuals")
-
-  if (ylim[[1]] == "default") {
-    ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE))
-  }
+  if (add && sep_obs) stop("If adding to an existing plot we can not show observed variables separately")
 
   solution_type = fit$solution_type
   parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
@@ -57,48 +55,90 @@ plot.mkinfit <- function(x, fit = x,
   out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, 
           solution_type = solution_type, atol = fit$atol, rtol = fit$rtol)
 
-  # Set up the plot if not to be added to an existing plot
-  if (add == FALSE) {
-    if (show_residuals) {
-      oldpar <- par(no.readonly = TRUE)
-      layout(matrix(c(1, 2), 2, 1), heights = c(2, 1.3))
-      par(mar = c(3, 4, 4, 2) + 0.1)
-    }
-    plot(0, type="n", 
-      xlim = xlim, ylim = ylim,
-      xlab = xlab, ylab = ylab, ...)
-  }
-  # Plot the data and model output
-  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
-  for (obs_var in obs_vars) {
-    points(subset(fit$data, variable == obs_var, c(time, observed)), 
-      pch = pch_obs[obs_var], col = col_obs[obs_var])
-  }
-  matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars])
-  if (legend == TRUE) {
-    legend_names = lapply(names(fit$mkinmod$spec), function(x) {
-                          if (!is.null(fit$mkinmod$spec[[x]]$full_name))
-                            if (is.na(fit$mkinmod$spec[[x]]$full_name)) x
-                            else fit$mkinmod$spec[[x]]$full_name
-                          else x
-      })
-    legend(lpos, inset= inset, legend = legend_names,
-      col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
+  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
+
+  # Create a plot layout only if not to be added to an existing plot
+  # or only a single plot is requested (e.g. by plot.mmkin)
+  do_layout = FALSE
+  if (show_residuals) do_layout = TRUE
+  if (sep_obs) do_layout = TRUE
+  n_plot_rows = if (sep_obs) length(obs_vars) else 1
+
+  if (do_layout) {
+    # Layout should be restored afterwards
+    oldpar <- par(no.readonly = TRUE)
+
+    n_plot_cols = if (show_residuals) 2 else 1
+    n_plots = n_plot_rows * n_plot_cols
+
+    # Set relative plot heights, so the first and the last plot are the norm
+    # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle
+    rel.heights <- if (n_plot_rows > 2) c(1, rep(rel.height.middle, n_plot_rows - 2), 1)
+                   else rep(1, n_plot_rows)
+    layout_matrix = matrix(1:n_plots, 
+                           n_plot_rows, n_plot_cols, byrow = TRUE)
+    layout(layout_matrix, heights = rel.heights)
   }
-  # Show residuals if requested
-  if (show_residuals) {
-    par(mar = c(5, 4, 0, 2) + 0.1)
-    residuals <- subset(fit$data, variable %in% obs_vars, residual)
-    if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
-    plot(0, type="n", 
-      xlim = xlim, 
-      ylim = c(-1.2 * maxabs, 1.2 * maxabs),
-      xlab = xlab, ylab = "Residuals")
-    for(obs_var in obs_vars){
-      residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual"))
-      points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
+
+  # Replicate legend position argument if necessary
+  if (length(lpos) == 1) lpos = rep(lpos, n_plot_rows)
+
+  # Loop over plot rows
+  for (plot_row in 1:n_plot_rows) {
+
+    row_obs_vars = if (sep_obs) obs_vars[plot_row] else obs_vars
+
+    # Set ylim to sensible default, or to the specified value
+    if (ylim[[1]] == "default") {
+      ylim_row = c(0, max(c(subset(fit$data, variable %in% row_obs_vars)$observed, 
+                        subset(fit$data, variable %in% row_obs_vars)$fitted), 
+                      na.rm = TRUE))
+    } else {
+      ylim_row = ylim
+    }
+
+    # Set up the main plot if not to be added to an existing plot
+    if (add == FALSE) {
+      plot(0, type="n", 
+        xlim = xlim, ylim = ylim_row,
+        xlab = xlab, ylab = ylab, ...)
+    }
+
+    # Plot the data
+    for (obs_var in row_obs_vars) {
+      points(subset(fit$data, variable == obs_var, c(time, observed)), 
+        pch = pch_obs[obs_var], col = col_obs[obs_var])
+    }
+
+    # Plot the model output
+    matlines(out$time, out[row_obs_vars], col = col_obs[row_obs_vars], lty = lty_obs[row_obs_vars])
+
+    if (legend == TRUE) {
+      # Get full names from model definition if they are available
+      legend_names = lapply(row_obs_vars, function(x) {
+                            if (!is.null(fit$mkinmod$spec[[x]]$full_name))
+                              if (is.na(fit$mkinmod$spec[[x]]$full_name)) x
+                              else fit$mkinmod$spec[[x]]$full_name
+                            else x
+        })
+      legend(lpos[plot_row], inset= inset, legend = legend_names,
+        col = col_obs[row_obs_vars], pch = pch_obs[row_obs_vars], lty = lty_obs[row_obs_vars])
+    }
+
+    # Show residuals if requested
+    if (show_residuals) {
+      residuals <- subset(fit$data, variable %in% row_obs_vars, residual)
+      if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
+      plot(0, type="n", 
+        xlim = xlim, 
+        ylim = c(-1.2 * maxabs, 1.2 * maxabs),
+        xlab = xlab, ylab = "Residuals")
+      for(obs_var in row_obs_vars){
+        residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual"))
+        points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
+      }
+      abline(h = 0, lty = 2)
     }
-    abline(h = 0, lty = 2)
-    par(oldpar, no.readonly = TRUE)
   }
+  if (do_layout) par(oldpar, no.readonly = TRUE)
 }
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index f701890a..44caf8d2 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -56,13 +56,19 @@ m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"),
 models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
 datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
 
-time_default <- system.time(fits <- mmkin(models, datasets))
+time_default <- system.time(fits.0 <- mmkin(models, datasets))
 time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))
 
 time_default
 time_1
 
 endpoints(fits[["SFO_lin", 2]])
+
+# Plot.mkinfit handles rows or columns of mmkin result objects
+plot(fits.0[1, ])
+# Double brackets to select a single mkinfit object, which will be
+# plotted by plot.mkinfit
+plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE)
 }
 }
 \keyword{ optimize }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 494dc38d..b80928f7 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -14,10 +14,11 @@
   xlab = "Time", ylab = "Observed", 
   xlim = range(fit$data$time),
   ylim = "default",
-  col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, 
-  lty_obs = rep(1, length(fit$mkinmod$map)),
+  col_obs = 1:length(obs_vars), pch_obs = col_obs, 
+  lty_obs = rep(1, length(obs_vars)),
   add = FALSE, legend = !add,
   show_residuals = FALSE, maxabs = "auto",
+  sep_vars = FALSE, rel.height.middle = 0.9,
   lpos = "topright", inset = c(0.05, 0.05), \dots)
 }
 \arguments{
@@ -25,7 +26,7 @@
     Alias for fit introduced for compatibility with the generic S3 method.  
   }
   \item{fit}{
-    an object of class \code{\link{mkinfit}}.
+    An object of class \code{\link{mkinfit}}.
   }
   \item{obs_vars}{
     A character vector of names of the observed variables for which the 
@@ -33,47 +34,54 @@
     in the model.
   }
   \item{xlab}{
-    label for the x axis.
+    Label for the x axis.
   }
   \item{ylab}{
-    label for the y axis.
+    Label for the y axis.
   }
   \item{xlim}{
-    plot range in x direction.
+    Plot range in x direction.
   }
   \item{ylim}{
-    plot range in y direction.
+    Plot range in y direction.
   }
   \item{col_obs}{
-    colors used for plotting the observed data and the corresponding model prediction lines.
+    Colors used for plotting the observed data and the corresponding model prediction lines.
   }
   \item{pch_obs}{
-    symbols to be used for plotting the data.
+    Symbols to be used for plotting the data.
   }
   \item{lty_obs}{
-    line types to be used for the model predictions.
+    Line types to be used for the model predictions.
   }
   \item{add}{
-    should the plot be added to an existing plot?
+    Should the plot be added to an existing plot?
   }
   \item{legend}{
-    should a legend be added to the plot?
+    Should a legend be added to the plot?
   }
   \item{show_residuals}{
-    should residuals be shown in the lower third of the plot?
+    Should residuals be shown in the lower third of the plot?
   }
   \item{maxabs}{
     Maximum absolute value of the residuals. This is used for the scaling of
     the y axis and defaults to "auto".
   }
+  \item{sep_obs}{
+    Should the observed variables be shown in separate subplots?
+  }
+  \item{rel.height.middle}{
+    The relative height of the middle plot, if more than two rows of plots are shown.
+  }
   \item{lpos}{
-    position of the legend. Passed to \code{\link{legend}} as the first argument.
+    Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument.
+    If not length one, this should be of the same length as the obs_var argument.
   }
   \item{inset}{
     Passed to \code{\link{legend}} if applicable.
   }
   \item{\dots}{
-   further arguments passed to \code{\link{plot}}.
+    Further arguments passed to \code{\link{plot}}.
   }
 }
 \value{
@@ -81,13 +89,18 @@
 }
 \examples{
 # One parent compound, one metabolite, both single first order, path from
-# parent to sink included
+# parent to sink included, use Levenberg-Marquardt for speed
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
                    m1 = mkinsub("SFO", full = "Metabolite M1" ))
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
 plot(fit)
+
+# Show the observed variables separately
+plot(fit, sep_obs = TRUE)
+
+# Show the observed variables separately, with residuals
+plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"))
 }
 \author{
   Johannes Ranke
 }
-\keyword{ hplot }
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 8362f16c..ffd83d2f 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -32,7 +32,7 @@
     Passed to the plot functions and \code{\link{mtext}}.
 }
   \item{rel.height.middle}{
-    The relative height of the middle plot.
+    The relative height of the middle plot, if more than two rows of plots are shown.
 }
   \item{\dots}{
     Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}.