Resolve TODOs and FIXMEs in plotting functions,

closes #20

NEWS.md

@@ -5,6 +5,7 @@
 * New function `predict_ecxsys()` replaces `fn()` from the `ecxsys` output.
 * Renamed the arguments in `ec()`.
 * Made `ec()` more flexible. It now also accepts a data.frame with a concentration column and a column of response values.
+* Mention LL5 curves in legend of `plot_effect()`.
 * Improved the internal structure of the package.
 * Improved the tests.
 * Improved documentation.

R/plot_effect.R

@@ -12,7 +12,7 @@ plot_effect <- function(model,
     )
     curves <- temp$curves
     log_ticks <- get_log_ticks(curves$concentration)
-    model$args$concentration[1] <- curves$concentration[1]
+    concentration <- c(curves$concentration[1], model$args$concentration[-1])
 
     plot(
         NA,
@@ -26,18 +26,19 @@ plot_effect <- function(model,
         bty = "L",
         las = 1
     )
+
     if (show_simple_model) {
         lines(
             curves$concentration,
             curves$effect_tox_simple,
-            col = rgb(112, 112, 207, maxColorValue = 255),
+            col = "darkblue",
             lty = 4
         )
         if (model$with_env) {
             lines(
                 curves$concentration,
                 curves$effect_tox_env_simple,
-                col = rgb(207, 112, 112, maxColorValue = 255),
+                col = "darkred",
                 lty = 4
             )
         }
@@ -48,63 +49,59 @@ plot_effect <- function(model,
         curves$effect_tox_sys,
         col = "blue"
     )
-    if (model$with_env) {
-        lines(
-            curves$concentration,
-            curves$effect_tox_env_sys,
-            col = "red"
-        )
-    }
     lines(
         curves$concentration,
         curves$effect_tox,
         col = "deepskyblue",
         lty = 2
     )
+    points(
+        concentration,
+        model$args$effect_tox_observed,
+        pch = 16,
+        col = "blue"
+    )
+
     if (model$with_env) {
+        lines(
+            curves$concentration,
+            curves$effect_tox_env_sys,
+            col = "red"
+        )
         lines(
             curves$concentration,
             curves$effect_tox_env,
             col = "orange",
             lty = 2
         )
-    }
-    points(
-        model$args$concentration,
-        model$args$effect_tox_observed,
-        pch = 16,
-        col = "blue"
-    )
-    if (model$with_env) {
-        # TODO: merge this with the same condition above.
         points(
-            model$args$concentration,
+            concentration,
             model$args$effect_tox_env_observed,
             pch = 16,
             col = "red"
         )
     }
+
     axis(1, at = log_ticks$major, labels = log_ticks$major_labels)
     axis(1, at = log_ticks$minor, labels = FALSE, tcl = -0.25)
     plotrix::axis.break(1, breakpos = temp$axis_break_conc)
+
     if (show_legend) {
-        # TODO: Maybe do proper subscript in legend
-        # TODO: Add simple models to the legend
-        legend_text <- c(
-            "effect (tox+sys)",
-            "effect (tox+env+sys)",
-            "toxicant effect",
-            "tox_env effect"
-        )
-        legend_pch <- c(16, 16, NA, NA)
-        legend_lty <- c(1, 1, 2, 2)
-        legend_col <- c("blue", "red", "deepskyblue", "orange")
-        if (!model$with_env) {
-            keep <- c(1, 3)
-            legend_text <- legend_text[keep]
-            legend_pch <- legend_pch[keep]
-            legend_lty <- legend_lty[keep]
-            legend_col <- legend_col[keep]
+        legend_text <- c("tox", "tox + sys")
+        legend_pch <- c(NA, 16)
+        legend_lty <- c(2, 1)
+        legend_col <- c("deepskyblue", "blue")
+        if (model$with_env) {
+            legend_text <- c(legend_text, "tox + env", "tox + env + sys")
+            legend_pch <- c(legend_pch, NA, 16)
+            legend_lty <- c(legend_lty, 2, 1)
+            legend_col <- c(legend_col, "orange", "red")
+        }
+        if (show_simple_model) {
+            legend_text <- c(legend_text, "tox (LL5)", "tox + env (LL5)")
+            legend_pch <- c(legend_pch, NA, NA)
+            legend_lty <- c(legend_lty, 4, 4)
+            legend_col <- c(legend_col, "darkblue", "darkred")
         }
         legend(
             "topright",

R/plot_system_stress.R

@@ -9,8 +9,7 @@ plot_system_stress <- function(model, show_legend = FALSE) {
     curves <- temp$curves
     axis_break_conc <- temp$axis_break_conc
     log_ticks <- get_log_ticks(curves$concentration)
-    # FIXME: Don't overwrite this arg. Make a new variable instead.
-    model$args$concentration[1] <- curves$concentration[1]
+    concentration <- c(curves$concentration[1], model$args$concentration[-1])
 
     plot(
         NA,
@@ -24,17 +23,19 @@ plot_system_stress <- function(model, show_legend = FALSE) {
         las = 1,
         bty = "L"
     )
+
     lines(
         curves$concentration,
         curves$sys_stress_tox,
         col = "blue"
     )
     points(
-        model$args$concentration,
+        concentration,
         model$sys_stress_tox,
         pch = 16,
         col = "blue"
     )
+
     if (model$with_env) {
         lines(
             curves$concentration,
@@ -42,25 +43,23 @@ plot_system_stress <- function(model, show_legend = FALSE) {
             col = "red"
         )
         points(
-            model$args$concentration,
+            concentration,
             model$sys_stress_tox_env,
             pch = 16,
             col = "red"
         )
     }
+
     axis(1, at = log_ticks$major, labels = log_ticks$major_labels)
     axis(1, at = log_ticks$minor, labels = FALSE, tcl = -0.25)
     plotrix::axis.break(1, breakpos = axis_break_conc)
+
     if (show_legend) {
-        legend_text <- c(
-            # TODO: Maybe do proper subscript in legend
-            "system stress (tox)",
-            "system stress (tox+env)"
-        )
-        legend_col <- c("blue", "red")
-        if (!model$with_env) {
-            legend_text <- legend_text[1]
-            legend_col <- legend_col[1]
+        legend_text <- c("tox")
+        legend_col <- c("blue")
+        if (model$with_env) {
+            legend_text <- c(legend_text, "tox + env")
+            legend_col <- c(legend_col, "red")
         }
         legend(
             "topright",