Some changes to improve plots on beamer slides

8 files changed, 41 insertions, 20 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index b95c33bd..bc8e61d6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
 Version: 0.9.49.6
-Date: 2019-07-05
+Date: 2019-09-02
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index 949776ca..477247b5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
-# mkin 0.9.49.6 (2019-07-08)
+# mkin 0.9.49.6 (unreleased)
+
+- Support frameless plots ('frame = FALSE')
+
+- Support to suppress the chi2 error level ('show_errmin = FALSE') in 'plot.mmkin'
 
 - Update README and the introductory vignette
 
diff --git a/R/mkinerrplot.R b/R/mkinerrplot.R
index cc163922..6153a3c0 100644
--- a/R/mkinerrplot.R
+++ b/R/mkinerrplot.R
@@ -23,6 +23,7 @@ mkinerrplot <- function (object,
   xlab = "Predicted", ylab = "Squared residual",
   maxy = "auto", legend= TRUE, lpos = "topright",
   col_obs = "auto", pch_obs = "auto",
+  frame = TRUE,
   ...)
 {
   obs_vars_all <- as.character(unique(object$data$variable))
@@ -48,7 +49,7 @@ mkinerrplot <- function (object,
   plot(0, type = "n",
        xlab = xlab, ylab = ylab,
        xlim = xlim,
-       ylim = c(0, 1.2 * maxy), ...)
+       ylim = c(0, 1.2 * maxy), frame = frame, ...)
 
   for(obs_var in obs_vars){
     residuals_plot <- subset(object$data, variable == obs_var, c("predicted", "residual"))
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index df9888e7..2a82301f 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -31,7 +31,8 @@ plot.mkinfit <- function(x, fit = x,
   maxabs = "auto",
   sep_obs = FALSE, rel.height.middle = 0.9,
   lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, ...)
+  show_errmin = FALSE, errmin_digits = 3, 
+  frame = TRUE, ...)
 {
   if (add && show_residuals) stop("If adding to an existing plot we can not show residuals")
   if (add && show_errplot) stop("If adding to an existing plot we can not show the error model plot")
@@ -138,7 +139,7 @@ plot.mkinfit <- function(x, fit = x,
     if (add == FALSE) {
       plot(0, type="n",
         xlim = xlim, ylim = ylim_row,
-        xlab = xlab, ylab = ylab, ...)
+        xlab = xlab, ylab = ylab, frame = frame, ...)
     }
 
     # Plot the data
@@ -197,7 +198,7 @@ plot.mkinfit <- function(x, fit = x,
       plot(0, type="n",
         xlim = xlim,
         ylim = c(-1.2 * maxabs_row, 1.2 * maxabs_row),
-        xlab = xlab, ylab = "Residuals")
+        xlab = xlab, ylab = "Residuals", frame = frame)
       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])
@@ -208,7 +209,7 @@ plot.mkinfit <- function(x, fit = x,
     # Show error model plot if requested
     if (show_errplot) {
       mkinerrplot(fit, obs_vars = row_obs_vars, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars],
-                  legend = FALSE)
+                  legend = FALSE, frame = frame)
     }
   }
   if (do_layout) par(oldpar, no.readonly = TRUE)
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index c9d98718..ef80949c 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -18,6 +18,7 @@
 
 plot.mmkin <- function(x, main = "auto", legends = 1, 
                        resplot = c("time", "errmod"),
+                       show_errmin = TRUE,
                        errmin_var = "All data", errmin_digits = 3,
                        cex = 0.7, rel.height.middle = 0.9, ...) {
   n.m <- nrow(x)
@@ -83,23 +84,27 @@ plot.mmkin <- function(x, main = "auto", legends = 1,
                        datasets = colnames(x)[i.fit],
                        none = "")
 
-    chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits)
-
-    # Use LateX if the current plotting device is tikz
-    if (names(dev.cur()) == "tikz output") {
-      chi2_text <- paste0(fit_name, " $\\chi^2$ error level = ", chi2, "\\%")
-    } else {
-      chi2_perc <- paste0(chi2, "%")
-      chi2_text <- bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2_perc))
+    if (show_errmin) {
+      chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits)
+
+      # Use LateX if the current plotting device is tikz
+      if (names(dev.cur()) == "tikz output") {
+        chi2_text <- paste0(fit_name, " $\\chi^2$ error level = ", chi2, "\\%")
+      } else {
+        chi2_perc <- paste0(chi2, "%")
+        chi2_text <- bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2_perc))
+      }
+      mtext(chi2_text, cex = cex, line = 0.4)
     }
-    mtext(chi2_text, cex = cex, line = 0.4)
 
     if (resplot == "time") {
       mkinresplot(fit, legend = FALSE, ...)
     } else {
       mkinerrplot(fit, legend = FALSE, ...)
     }
-    mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4)
+    if (show_errmin) {
+      mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4)
+    }
   }
 
   par(oldpar, no.readonly = TRUE)
diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd
index 3b557b0a..37338d01 100644
--- a/man/mkinerrplot.Rd
+++ b/man/mkinerrplot.Rd
@@ -18,6 +18,7 @@
     xlab = "Predicted", ylab = "Squared residual",
     maxy = "auto", legend= TRUE, lpos = "topright",
     col_obs = "auto", pch_obs = "auto",
+    frame = TRUE,
     ...)
 }
 \arguments{
@@ -54,6 +55,9 @@
   \item{pch_obs}{
     Symbols to be used for the observed variables.
   }
+  \item{frame}{
+    Should a frame be drawn around the plots?
+  }
   \item{\dots}{
    further arguments passed to \code{\link{plot}}.
   }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 5e20ad90..a4f47073 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -27,7 +27,7 @@
   maxabs = "auto",
   sep_obs = FALSE, rel.height.middle = 0.9,
   lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, \dots)
+  show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots)
 plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, \dots)
 }
 \arguments{
@@ -105,6 +105,9 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, \dots)
   \item{errmin_digits}{
     The number of significant digits for rounding the FOCUS chi2 error percentage.
   }
+  \item{frame}{
+    Should a frame be drawn around the plots?
+  }
   \item{\dots}{
     Further arguments passed to \code{\link{plot}}.
   }
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 44e5e4c7..90b92d27 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -13,8 +13,8 @@
 }
 \usage{
 \method{plot}{mmkin}(x, main = "auto", legends = 1,
-  resplot = c("time", "errmod"), errmin_var = "All data", errmin_digits = 3,
-  cex = 0.7, rel.height.middle = 0.9, ...)
+  resplot = c("time", "errmod"), show_errmin = TRUE, errmin_var = "All data", 
+  errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...)
 }
 \arguments{
   \item{x}{
@@ -31,6 +31,9 @@
     or as squared residuals against predicted values, with the error model,
     using \code{\link{mkinerrplot}}.
 }
+  \item{show_errmin}{
+    Should the chi2 error level be shown on top of the plots to the left?
+  }
   \item{errmin_var}{
     The variable for which the FOCUS chi2 error value should be shown.
 }