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.

1 files changed, 88 insertions, 48 deletions

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)
 }