Alex Koiter
In [1]:
suppressPackageStartupMessages({
library(tidyverse)
library(terra)
library(patchwork)
library(sf)
})Warning: package 'ggplot2' was built under R version 4.4.3Warning: package 'terra' was built under R version 4.4.3Warning: package 'patchwork' was built under R version 4.4.2In [2]:
ag_data <- read_csv(here::here("./notebooks/ag_terrain_data.csv"), show_col_types = FALSE)
forest_data <- read_csv(here::here("./notebooks/forest_terrain_data.csv"), show_col_types = FALSE) In [3]:
theme_right <- theme(axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = "right",
legend.box.spacing = unit(0, "pt"),
legend.margin = margin(0,0,0,3),
legend.justification = "left",
legend.title = element_text(hjust = 0))
theme_left <- theme(axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = "left",
legend.text.position = "left",
legend.box.spacing = unit(0, "pt"),
legend.margin=margin(0,3,0,0),
legend.justification="right",
legend.title = element_text(hjust = 1))
theme_bottom <- theme(axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = "bottom",
legend.text.position = "bottom",
legend.box.spacing = unit(0, "pt"),
legend.margin=margin(3,0,0,0),
legend.justification="top")In [4]:
ag_rast <- rast(ag_data)
crs(x = ag_rast, warn=FALSE) <- "epsg:26914"
coords <- read_csv(here::here("./notebooks/coords.csv"), show_col_types = FALSE) %>%
st_as_sf(coords = c("long", "lat"), crs = 4326) %>%
st_transform(crs = 26914)
a_col <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = a_c)) +
scale_fill_viridis_c(name = bquote(italic("a*")), breaks = seq(2.5, 4, 0.5)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
b_col <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = b_c)) +
scale_fill_viridis_c(name = bquote(italic("b*")), breaks = seq(7, 10, 1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
c_col <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = c_c)) +
scale_fill_viridis_c(name = bquote(italic("c*")), breaks = seq(7, 11, 1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
h_col <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = h_c)) +
scale_fill_viridis_c(name = bquote(italic("h*")), breaks = seq(1.15, 1.25, 0.02)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
x_col <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = x_c)) +
scale_fill_viridis_c(name = bquote(italic("x")), breaks = seq(0.470, 0.476, 0.003)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
ca <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = ca)) +
scale_fill_viridis_c(name = "Ca") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
co <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = co)) +
scale_fill_viridis_c(name = "Co", breaks = seq(8, 11, 1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
cs <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = cs)) +
scale_fill_viridis_c(name = "Cs", breaks = seq(0.5, 1.1, 0.2), limits = c(0.4, 1.1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
fe <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = fe)) +
scale_fill_viridis_c(name = "Cs") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
li <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = li)) +
scale_fill_viridis_c(name = "Li", breaks = seq(14, 20, 2), limits = c(13, 20)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
la <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = la)) +
scale_fill_viridis_c(name = "La", breaks = seq(16, 20, 1), limits = c(16, 20)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
nb <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = nb)) +
scale_fill_viridis_c(name = "Nb", breaks = seq(0.5, 0.7, 0.1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
ni <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = ni)) +
scale_fill_viridis_c(name = "Ni") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
rb <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = rb)) +
scale_fill_viridis_c(name = "Rb") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
sr <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = sr)) +
scale_fill_viridis_c(name = "Sr") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))In [5]:
dem <- ggplot() +
tidyterra::geom_spatraster(data = ag_rast, aes(fill = elevation)) +
scale_fill_viridis_c(name = "Elev.", option = "inferno", limits = c(309, 312)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
#
# ssa <- ggplot() +
# tidyterra::geom_spatraster(data = ag_rast, aes(fill = ssa)) +
# scale_fill_viridis_c(name = "SSA") +
# #geom_sf(data = filter(coords, site == "Agriculture")) +
# theme_minimal(base_size = 12) +
# theme_right +
# scale_y_continuous(expand = c(0,0)) +
# scale_x_continuous(expand = c(0,0))
#
# organic <- ggplot() +
# tidyterra::geom_spatraster(data = ag_rast, aes(fill = organic)) +
# scale_fill_viridis_c(name = "Organic") +
# #geom_sf(data = filter(coords, site == "Agriculture")) +
# theme_minimal(base_size = 12) +
# theme_left +
# scale_y_continuous(expand = c(0,0)) +
# scale_x_continuous(expand = c(0,0))
scale_p <- ggplot() +
geom_sf(data = filter(coords, site == "Agriculture"), colour = "white") +
theme_void(base_size = 12)+
ggspatial::annotation_scale(location = "bl", width_hint = 0.4) +
ggspatial::annotation_north_arrow(location = "bl", pad_y = unit(2, "cm"))In [6]:
p_ag <- ca + co + cs + fe + li + la + nb + ni + rb + sr + a_col + b_col + c_col + h_col + x_col + dem + plot_layout(ncol = 4)
p_ag
#ggsave(filename = "../Submission/Figure 2.png", plot = p_ag, height = 240, width = 190, units = "mm", dpi = 600)
In [7]:
forest_rast <- rast(forest_data)
crs(x = forest_rast, warn=FALSE) <- "epsg:26914"
h_col_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = h_c)) +
scale_fill_viridis_c(name = bquote(italic("h*"))) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
ca_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = ca)) +
scale_fill_viridis_c(name = "Ca", breaks = seq(1, 3, 1)) +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
co_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = co)) +
scale_fill_viridis_c(name = "Co") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
cs_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = cs)) +
scale_fill_viridis_c(name = "Cs") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
la_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = la)) +
scale_fill_viridis_c(name = "La") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
li_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = li)) +
scale_fill_viridis_c(name = "Li") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
nb_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = nb)) +
scale_fill_viridis_c(name = "Nb", breaks = c(0.3, 0.35, 0.4)) +
#geom_sf(data = filter(coords, site == "Forest")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
ni_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = ni)) +
scale_fill_viridis_c(name = "Ni", breaks = seq(15, 23, 2)) +
#geom_sf(data = filter(coords, site == "Forest")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
sr_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = sr)) +
scale_fill_viridis_c(name = "Sr") +
#geom_sf(data = filter(coords, site == "Forest")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0)) In [8]:
dem_forest <- ggplot() +
tidyterra::geom_spatraster(data = forest_rast, aes(fill = elevation)) +
scale_fill_viridis_c(name = "Elev.", option = "inferno") +
#geom_sf(data = filter(coords, site == "Agriculture")) +
theme_minimal(base_size = 12) +
theme_bottom +
scale_y_continuous(expand = c(0,0)) +
scale_x_continuous(expand = c(0,0))
# ssa_forest <- ggplot() +
# tidyterra::geom_spatraster(data = forest_rast, aes(fill = ssa)) +
# scale_fill_viridis_c(name = "SSA") +
# #geom_sf(data = filter(coords, site == "Agriculture")) +
# theme_minimal(base_size = 12) +
# theme_right +
# scale_y_continuous(expand = c(0,0)) +
# scale_x_continuous(expand = c(0,0))
#
# organic_forest <- ggplot() +
# tidyterra::geom_spatraster(data = forest_rast, aes(fill = organic)) +
# scale_fill_viridis_c(name = "Organic") +
# #geom_sf(data = filter(coords, site == "Agriculture")) +
# theme_minimal(base_size = 12) +
# theme_left +
# scale_y_continuous(expand = c(0,0)) +
# scale_x_continuous(expand = c(0,0))
scale_p_forest <- ggplot() +
geom_sf(data = filter(coords, site == "Forest"), colour = "white") +
theme_void(base_size = 12)+
ggspatial::annotation_scale(location = "bl", width_hint = 0.3) +
ggspatial::annotation_north_arrow(location = "bl", pad_y = unit(2, "cm"))In [9]:
p_for <- ca_forest + co_forest + cs_forest + la_forest + li_forest + nb_forest + ni_forest + sr_forest + h_col_forest + dem_forest +
plot_layout(ncol = 4)
p_for
#ggsave(filename = "../Submission/Figure 3.png", plot = p_for, height = 175, width = 190, units = "mm", dpi = 600)