3rd revision

R/fig1.R

@@ -44,8 +44,8 @@ p1 <- ggplot() +
   # scale_color_brewer(palette = "BuPu") +
   labs(fill = "") +
   labs(color = "Sampling\ndistance (m)") +
-  xlab("x-distance (m)") +
-  ylab("y-distance (m)") +
+  xlab(bquote(italic(x)*"-distance (m)")) +
+  ylab(bquote(italic(y)*"-distance (m)")) +
   geom_segment(data = configuration, aes(x = 0, y = 0, xend = x, yend = y, group = radius), size = 0.25) +
   geom_label(data = configuration, aes(x = x, y = y, label = sprintf("%2.0f%% melt pond cover", radius * 100)), hjust = 0, label.size = 0, nudge_x = 1, size = 2, label.padding = unit(0.05, "lines")) +
   guides(color = guide_legend(
@@ -97,7 +97,7 @@ p2 <- ggplot() +
   annotate("segment", x = -75, xend = -65, y = 0, yend = -10, lty = 1, size = 0.25, arrow = arrow(length = unit(1.5, "mm")), color = "orange") +
 
   annotate("text", x = -110, y = -100, label = "Homogeneous water column:", size = 3.5, hjust = 0, fontface = 2, family = "IBM Plex Sans Light") +
-  annotate("text", x = -110, y = -110, label = expression("a = b = 0.05"*m^{-1}), size = 3, hjust = 0, family = "IBM Plex Sans Light") +
+  annotate("text", x = -110, y = -110, label = expression(italic(a)*"="*italic(b)*"="*0.05*m^{-1}), size = 3, hjust = 0, family = "IBM Plex Sans Light", parse = TRUE) +
   annotate("text", x = -110, y = -120, label = "VSF: Fourrier-Forand 3%", size = 3, hjust = 0, family = "IBM Plex Sans Light") +
 
   theme(panel.grid = element_blank()) +

R/fig3.R

@@ -28,7 +28,7 @@ p1 <- df %>%
   geom_path() +
   scale_y_reverse() +
   ylab("Depth (m)") +
-  xlab(bquote(E[d]~"("*mu*W~cm^{-2}*")")) +
+  xlab(bquote(italic(E[d])~"("*mu*W~cm^{-2}*")")) +
   labs(color = "Wavelengths (nm)") +
   theme(legend.position = "none") +
   guides(color = guide_legend(
@@ -46,7 +46,7 @@ p2 <- df %>%
   geom_path() +
   scale_y_reverse() +
   ylab("Depth (m)") +
-  xlab(bquote(L[u]~"("*mu*W~cm^{-2}~sr^{-1}*")")) +
+  xlab(bquote(italic(L[u])~"("*mu*W~cm^{-2}~sr^{-1}*")")) +
   labs(color = "Wavelengths (nm)") +
   theme(
   legend.position = c(0.99, 0.01),

R/fig4.R

@@ -51,8 +51,8 @@ p <- df %>%
     breaks = c("edz", "luz"),
     values = c(1, 2),
     labels = c(
-      bquote(Downwelling~irradiance~(E[d])),
-      bquote(Upwelling~radiance~(L[u]))
+      bquote(Downward~irradiance~(italic(E[d]))),
+      bquote(Upward~radiance~(italic(L[u])))
     )
   ) +
   guides(colour = FALSE)

R/fig5.R

@@ -49,8 +49,8 @@ p <- k2 %>%
   geom_point(aes(color = factor(wavelength)), size = 1) +
   geom_smooth(method = "lm", se = FALSE, size = 0.5, color = "red") +
   geom_abline(slope = 1, intercept = 0, lty = 2, color = "grey50") +
-  xlab(bquote(K[Lu]~(m^{-1}))) +
-  ylab(bquote(K[d]~(m^{-1}))) +
+  xlab(bquote(italic(K[Lu])~(m^{-1}))) +
+  ylab(bquote(italic(K[d])~(m^{-1}))) +
   labs(color = "Wavelength (nm)") +
   scale_color_manual(values = color) +
   facet_wrap(~depth_range, scales = "free", ncol = 3, labeller = as_labeller(appender)) +
@@ -95,8 +95,8 @@ p <- k2 %>%
   geom_point(aes(color = factor(wavelength)), size = 1) +
   geom_smooth(method = "lm", se = FALSE, size = 0.5, color = "red") +
   geom_abline(slope = 1, intercept = 0, lty = 2, color = "grey50") +
-  xlab(bquote(K[Lu]~(m^{-1}))) +
-  ylab(bquote(K[d]~(m^{-1}))) +
+  xlab(bquote(italic(K[Lu])~(m^{-1}))) +
+  ylab(bquote(italic(K[d])~(m^{-1}))) +
   labs(color = "Wavelength (nm)") +
   scale_color_manual(values = color) +
   facet_wrap(~depth_range, scales = "free", ncol = 3) +

R/fig6.R

@@ -151,7 +151,7 @@ iso <- df %>%
   drop_na()
 
 p <- df %>%
-  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Downward~irradiance~(E[d])", "Upward~radiance~(L[u])")) %>% 
+  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Downward~irradiance~(italic(E[d]))", "Upward~radiance~(italic(L[u]))")) %>% 
   ggplot(aes(x = x, y = y, fill = z, z = z)) +
   geom_raster() +
   scale_y_reverse(expand = c(0, 0), name = "Depth (m)") +

R/fig7-11.R

@@ -59,7 +59,7 @@ p1 <- simulo %>%
   theme(legend.key.size = unit(0.75, "lines")) +
   # theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
   theme(legend.position = "none") +
-  xlab("Downward irradiance (a.u.)")
+  xlab("Downward irradiance")
 
 p2 <- simulo %>%
   filter(source == "Radiance (Lu)") %>% 
@@ -74,7 +74,7 @@ p2 <- simulo %>%
   theme(legend.title = element_text(size = 8), legend.text = element_text(size = 6)) +
   theme(legend.key.size = unit(0.75, "lines")) +
   # theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
-  xlab("Upward radiance (a.u.)")
+  xlab("Upward radiance")
 
 p <- p1 +
   p2 +
@@ -195,7 +195,7 @@ p1 <- averaged_simulo %>%
   theme(legend.key.size = unit(0.5, "lines")) +
   scale_x_continuous(labels = scientific_10x) +
   ylab("Depth (m)") +
-  xlab("Downward irradiance (a.u.)") +
+  xlab("Downward irradiance") +
   theme(axis.text.x = element_text(angle = 35, hjust = 1)) +
   theme(legend.position = "none")
 
@@ -211,7 +211,7 @@ p2 <- averaged_simulo %>%
   theme(legend.key.size = unit(0.5, "lines")) +
   scale_x_continuous(labels = scientific_10x) +
   ylab("Depth (m)") +
-  xlab("Upward radiance (a.u.)") +
+  xlab("Upward radiance") +
   theme(axis.text.x = element_text(angle = 35, hjust = 1)) +
   theme(legend.margin = margin(t = 1, unit = 'cm'))
 
@@ -247,12 +247,12 @@ p <- k %>%
   xlab("Distance from the center of the melt pond (m)") +
   ylab(bquote("Attenuation coefficient"~(m^{-1}))) +
   theme(legend.position = c(0.95, 0.95), legend.justification = c(1, 1)) +
-  labs(color = "Radiometric quantity") +
   scale_color_manual(
     breaks = c("Irradiance (Ed)", "Radiance (Lu)"),
     values = RColorBrewer::brewer.pal(3, "Set1"),
-    labels = c(bquote(Downward~irradiance~(E[d])), bquote(Upward~radiance~(L[u])))
-  )
+    labels = c(bquote(italic(K[d])), bquote(italic(K[Lu])))
+  ) +
+  theme(legend.title = element_blank())
 
 ggsave("graphs/fig9.pdf", width = 5.5, height = 4, device = cairo_pdf)
 
@@ -290,10 +290,10 @@ labels <- c(
 )
 
 predicted_light2 <- predicted_light %>% 
-  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~K[d]", "Propagated~with~K[Lu]"))
+  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~italic(K[d])", "Propagated~with~italic(K[Lu])"))
 
 p <- reference_profile %>%
-  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~K[d]", "Propagated~with~K[Lu]")) %>% 
+  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~italic(K[d])", "Propagated~with~italic(K[Lu])")) %>% 
   ggplot(aes(x = value, y = depth)) +
   facet_grid(range ~ source2, scales = "free", labeller = labeller(source2 = label_parsed, range = label_value)) +
   scale_y_reverse() +
@@ -302,7 +302,7 @@ p <- reference_profile %>%
   labs(color = str_wrap("Distance from the center of the melt pond (m)", 20)) +
   scale_x_continuous(labels = scientific_10x, breaks = c(0, 3, 6)*1e6, limits = c(0, NA), expand = c(0.15, 0)) +
   ylab("Depth (m)") +
-  xlab("Downward irradiance (a.u.)") +
+  xlab("Downward irradiance") +
   theme(strip.text.y = element_text(size = 8)) +
   guides(col = guide_legend(ncol = 2)) +
   theme_bw(base_family = "IBM Plex Sans Light")
@@ -330,7 +330,7 @@ res <- left_join(int1, int2, by = c("source", "range")) %>%
 p <- res %>%
   spread(type, integral) %>%
   mutate(relative_error = (reference - predicted) / reference) %>%
-  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~K[d]", "Propagated~with~K[Lu]")) %>% 
+  mutate(source2 = ifelse(source == "Irradiance (Ed)", "Propagated~with~italic(K[d])", "Propagated~with~italic(K[Lu])")) %>% 
   ggplot(aes(x = mid_distance, y = relative_error, color = range)) + 
   geom_line() +
   # geom_point(show.legend = FALSE) +

R/supp_fig_4-6.R

@@ -53,7 +53,7 @@ p1 <- res2 %>%
   geom_point() +
   geom_ribbon(aes(ymin = r_squared_mean - r_squared_sd, ymax = r_squared_mean + r_squared_sd), alpha = 0.25) +
   xlab("Wavelength (nm)") +
-  ylab(bquote(atop("Determination", "coefficient" ~ "("*R ^ 2*")"))) +
+  ylab(bquote(atop("Determination", "coefficient" ~ "("*italic(R^2)*")"))) +
   scale_x_continuous(breaks = seq(400, 700, by = 50))
 
 p2 <- res2 %>%
@@ -124,8 +124,8 @@ p <- df %>%
   geom_point(size = 0.25, alpha = 0.5) +
   facet_wrap(~simulation_type) +
   scale_color_manual(values = color) +
-  ylab(bquote(K[d]~(m^{-1}))) +
-  xlab(bquote(K[Lu]~(m^{-1}))) +
+  ylab(bquote(italic(K[d])~(m^{-1}))) +
+  xlab(bquote(italic(K[Lu])~(m^{-1}))) +
   labs(color = "Wavelength (nm)") +
   geom_abline(lty = 2, size = 0.25) +
   guides(color = guide_legend(