This theme will produce ggplots that follow NAFO plot guidelines:
Font: Cambria 9pt.
Plot Border: black 0.5 pt. No borders around entire graph, just plot. Borders around legend (0.5pt) if possible.
Tick Marks to the inside on x & y axis
Graph lines: 0.75 pt, black if possible, otherwise grey
Plot size: Height 6.4 cm, width 11.5 cm.
The helper values .nafo_lwd, .nafo_height, and .nafo_width can be used to impose consistent graph line widths, plot heights, and plot widths, respectively.
theme_nafo(base_size = 9, base_family = "Cambria")See also
ggplot2::theme_minimal
Examples
library(ggplot2)
library(patchwork)
showtext::showtext_opts(dpi = 96) # Adjust dpi to match your plotting device (e.g., set to 300 if using ggsave with dpi set to 300)
theme_set(theme_nafo()) # set default ggplot2 theme
## Example of a summary plot ---------------------------------------------------
C_plot <- ggplot(aes(x = year), data = toy_stock) +
geom_bar(aes(y = catch, fill = "Catch"), stat = "identity", alpha = 0.4) +
geom_step(aes(x = year - 0.5, y = ifelse(year > 2015, 0, TAC), linetype = "TAC"), color = .nafo_cols[2]) +
scale_y_continuous(n.breaks = 10, name = "Catch / TAC", expand = expansion(c(0.01, 0.05))) +
scale_x_continuous(n.breaks = 10, name = "", expand = expansion(c(0.01, 0.01))) +
scale_fill_nafo() +
theme(legend.title = element_blank(),
legend.spacing.y = unit(0.1, "cm"))
B_plot <- ggplot(aes(x = year), data = toy_stock) +
geom_ribbon(aes(ymin = relB_lwr, ymax = relB_upr), fill = .nafo_cols[1], alpha = 0.4) +
geom_line(aes(y = relB), color = .nafo_cols[1]) +
scale_y_continuous(limits = c(0, NA), n.breaks = 10, name = "B/Blim", expand = expansion(c(0.01, 0.05))) +
scale_x_continuous(n.breaks = 10, name = "", expand = expansion(c(0.01, 0.01)))
F_plot <- ggplot(aes(x = year), data = toy_stock) +
geom_ribbon(aes(ymin = relF_lwr, ymax = relF_upr), fill = .nafo_cols[1], alpha = 0.4) +
geom_line(aes(y = relF), color = .nafo_cols[1]) +
scale_y_continuous(limits = c(0, NA), n.breaks = 10, name = "F/Flim", expand = expansion(c(0.01, 0.05))) +
scale_x_continuous(n.breaks = 10, name = "", expand = expansion(c(0.01, 0.01)))
R_plot <- ggplot(aes(x = year), data = toy_stock) +
geom_line(aes(y = rec_index1, color = "Survey 1")) +
geom_line(aes(y = rec_index2, color = "Survey 2")) +
geom_line(aes(y = rec_index3, color = "Survey 3")) +
scale_y_continuous(limits = c(0, NA), name = "Recruitment index", expand = expansion(c(0.01, 0.05))) +
scale_x_continuous(n.breaks = 10, name = "", expand = expansion(c(0.01, 0.01))) +
scale_color_nafo() +
theme(legend.title = element_blank())
summary_plot <- (C_plot + B_plot) / (F_plot + R_plot)
summary_plot
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## Facet plot of multiple species ----------------------------------------------
set.seed(123)
years <- rep(1990:2020, times = 4)
species <- rep(c("Cod", "Plaice", "Redfish", "Halibut"), each = length(unique(years)))
biomass <- exp(cumsum(rnorm(length(years), sd = 0.1)))
error <- exp(rnorm(length(years), mean = log(0.1), sd = 0.5))
lwr <- exp(log(biomass) - error)
upr <- exp(log(biomass) + error)
species_trends <- data.frame(year = years, species = species, biomass = biomass, lwr = lwr, upr = upr)
species_trends[species_trends$year %in% sample(unique(years), 5), c("biomass", "lwr", "upr")] <- NA
species_plot <- ggplot(aes(x = year, color = species), data = species_trends) +
geom_line(aes(y = biomass), linewidth = .nafo_lwd, linetype = 3) +
geom_segment(aes(xend = year, y = lwr, yend = upr), linewidth = .nafo_lwd) +
geom_point(aes(y = biomass), shape = 21, fill = "white") +
facet_wrap(~ species, scales = "free") +
scale_y_continuous(limits = c(0, NA), name = "Biomass index", expand = expansion(c(0.01, 0.05))) +
scale_x_continuous(n.breaks = 10, name = "Year", expand = expansion(c(0.02, 0.02))) +
scale_color_nafo(name = "Species") +
theme(legend.position = "none")
species_plot
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_point()`).
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if (interactive()) {
showtext::showtext_opts(dpi = 300)
ggsave("summary_plot.png", plot = summary_plot, height = .nafo_height * 2, width = .nafo_width * 2)
ggsave("species_plot.png", plot = species_plot, height = .nafo_height * 2, width = .nafo_width * 2)
}