diff --git a/findex/_targets.R b/findex/_targets.R
index 59f1a6d785a4a898d351f0ad275d86449cbd0515..81e686d6273402692e6ed29217941d732ddcc6ed 100644
--- a/findex/_targets.R
+++ b/findex/_targets.R
@@ -145,21 +145,23 @@ p3 <- list(
p3_threat_map_png,
{
final_plot <- threat_map(in_dat = p2_mean_weighted_threats,
- threat_category = p2_threat_categories,
- threat_pal = p3_color_pal,
- hybas_habitat_types = p2_hybas_habitat_types_sf,
- proj = p1_proj) +
+ threat_category = p2_threat_categories,
+ threat_pal = p3_color_pal,
+ hybas_habitat_types = p2_hybas_habitat_types_sf,
+ proj = p1_proj) +
theme(legend.position = "none")
- out_file <- paste0("../src/assets/images/", str_replace_all(p2_threat_categories, " ", "_"), "_map.png")
-
- ggsave(out_file,
- final_plot, height = 6, width = 10, dpi = 300)
+ save_map(type = "threat", plot = final_plot,
+ threat_category = p2_threat_categories,
+ subcat_habitat = NA,
+ subcat_pollution = NA,
+ subcat_climate = NA
+ )
},
format = "file",
pattern = p2_threat_categories
),
- tar_target(
+ tar_target( # will turn this into a function
p3_legend_png,
{
final_plot <- threat_map(in_dat = p2_mean_weighted_threats,
@@ -168,21 +170,16 @@ p3 <- list(
proj = p1_proj,
hybas_habitat_types = p2_hybas_habitat_types_sf)
- plot_legend <- get_plot_component(final_plot, "guide-box-right", return_all = T)
-
- out_file <- paste0("out/", str_replace_all(p2_threat_categories, " ", "_"), "_legend_raw.png")
-
- ggsave(out_file,
- plot_legend, dpi = 300, bg = "transparent")
- knitr::plot_crop(out_file)
-
- out_file_final <- paste0("../src/assets/images/", str_replace_all(p2_threat_categories, " ", "_"), "_legend.png")
-
- cowplot_legend(in_dat = p2_mean_weighted_threats, legend_png = out_file, threat_category = p2_threat_categories, out_file = out_file_final)
+ save_legend(type = "threat", plot = final_plot,
+ threat_category = p2_threat_categories,
+ subcat_habitat = NA,
+ subcat_pollution = NA,
+ subcat_climate = NA,
+ in_dat = p2_mean_weighted_threats)
},
pattern = p2_threat_categories
),
- tar_target( # will turn this into a function
+ tar_target(
p3_sub_threat_map_png,
{
final_plot <- subThreat_map(in_dat = p2_mean_weighted_subThreats,
@@ -195,20 +192,11 @@ p3 <- list(
hybas_habitat_types = p2_hybas_habitat_types_sf) +
theme(legend.position = "none")
- if(p2_threat_subcategories %in% p2_habitat_subthreats){
- out_file <- paste0("../src/assets/images/H_", str_replace_all(p2_threat_subcategories, " ", "_"), "_map.png")
- } else if(p2_threat_subcategories %in% p2_pollution_subthreats){
- out_file <- paste0("../src/assets/images/P_", str_replace_all(p2_threat_subcategories, " ", "_"), "_map.png")
- } else if(p2_threat_subcategories == "Overfishing"){
- out_file <- paste0("../src/assets/images/E_", str_replace_all(p2_threat_subcategories, " ", "_"), "_map.png")
- } else if(p2_threat_subcategories == "Invasive non-native species"){
- out_file <- paste0("../src/assets/images/IS_", str_replace_all(p2_threat_subcategories, " ", "_"), "_map.png")
- } else if(p2_threat_subcategories %in% p2_climate_subthreats){
- out_file <- paste0("../src/assets/images/CW_", str_replace_all(p2_threat_subcategories, " ", "_"), "_map.png")
- }
-
- ggsave(out_file,
- final_plot, height = 6, width = 10, dpi = 300)
+ save_map(type = "threat", plot = final_plot,
+ threat_category = p2_threat_subcategories,
+ subcat_habitat = p2_habitat_subthreats,
+ subcat_pollution = p2_pollution_subthreats,
+ subcat_climate = p2_climate_subthreats)
},
format = "file",
pattern = p2_threat_subcategories
@@ -225,37 +213,12 @@ p3 <- list(
proj = p1_proj,
hybas_habitat_types = p2_hybas_habitat_types_sf)
- plot_legend <- get_plot_component(final_plot, "guide-box-right", return_all = T)
-
- if(p2_threat_subcategories %in% p2_habitat_subthreats){
- out_file <- paste0("out/H_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend_raw.png")
- } else if(p2_threat_subcategories %in% p2_pollution_subthreats){
- out_file <- paste0("out/P_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend_raw.png")
- } else if(p2_threat_subcategories == "Overfishing"){
- out_file <- paste0("out/E_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend_raw.png")
- } else if(p2_threat_subcategories == "Invasive non-native species"){
- out_file <- paste0("out/IS_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend_raw.png")
- } else if(p2_threat_subcategories %in% p2_climate_subthreats){
- out_file <- paste0("out/CW_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend_raw.png")
- }
-
- ggsave(out_file,
- plot_legend, dpi = 300, bg = "transparent")
- knitr::plot_crop(out_file)
-
- if(p2_threat_subcategories %in% p2_habitat_subthreats){
- out_file_final <- paste0("../src/assets/images/H_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend.png")
- } else if(p2_threat_subcategories %in% p2_pollution_subthreats){
- out_file_final <- paste0("../src/assets/images/P_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend.png")
- } else if(p2_threat_subcategories == "Overfishing"){
- out_file_final <- paste0("../src/assets/images/E_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend.png")
- } else if(p2_threat_subcategories == "Invasive non-native species"){
- out_file_final <- paste0("../src/assets/images/IS_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend.png")
- } else if(p2_threat_subcategories %in% p2_climate_subthreats){
- out_file_final <- paste0("../src/assets/images/CW_", str_replace_all(p2_threat_subcategories, " ", "_"), "_legend.png")
- }
-
- cowplot_legend(in_dat = p2_mean_weighted_subThreats, legend_png = out_file, threat_category = p2_threat_subcategories, out_file = out_file_final)
+ save_legend(type = "subThreat", plot = final_plot,
+ threat_category = p2_threat_subcategories,
+ subcat_habitat = p2_habitat_subthreats,
+ subcat_pollution = p2_pollution_subthreats,
+ subcat_climate = p2_climate_subthreats,
+ in_dat = p2_mean_weighted_subThreats)
},
format = "file",
pattern = p2_threat_subcategories
diff --git a/findex/src/plot_utils.R b/findex/src/plot_utils.R
index f103b46c84b6f3b5a7bbd6139b1bc11ad1461d2e..187a58e4657bb8667262d83598c9de7e522909e1 100644
--- a/findex/src/plot_utils.R
+++ b/findex/src/plot_utils.R
@@ -1,61 +1,4 @@
-threat_map <- function(in_dat, threat_category, threat_pal, hybas_habitat_types, proj){
-# hybas_habitat_types = p2_hybas_habitat_types_sf
-filtered_df <- in_dat |>
- left_join(hybas_habitat_types) |>
- st_as_sf() |>
- dplyr::filter(ThreatCategory == threat_category) |>
- # remove visual bug with robinson projection
- st_wrap_dateline()
-
-proj_df <- st_transform(filtered_df, crs = st_crs(proj))
-
-if(threat_category == "Habitat"){
- pal <- threat_pal$Habitat_pal
-} else if(threat_category == "Pollution"){
- pal <- threat_pal$Pollution_pal
-} else if(threat_category == "Exploitation"){
- pal <- threat_pal$Exploitation_pal
-} else if(threat_category == "Invasive species"){
- pal <- threat_pal$Invasive_pal
-} else if(threat_category == "Climate and weather"){
- pal <- threat_pal$Climate_pal
-}
-
-threat_map <- ggplot()+
- geom_sf(data = proj_df, aes(geometry = Shape, fill = MeanWeightedThreatMetric, color = MeanWeightedThreatMetric))+
- scale_fill_gradientn(
- colors = colorRampPalette(c(rev(unlist(pal))))(100),
- limits = c(0, max(proj_df$MeanWeightedThreatMetric, na.rm = T)),
- na.value = "gray80",
- breaks = c(0 + max(proj_df$MeanWeightedThreatMetric, na.rm = T)/10,
- #max(habitat_data$MeanWeightedThreatMetric)/2,
- max(proj_df$MeanWeightedThreatMetric, na.rm = T) - max(proj_df$MeanWeightedThreatMetric, na.rm = T)/10),
- labels = c("Lower", "Higher")
- )+
- scale_color_gradientn(
- colors = colorRampPalette(c(rev(unlist(pal))))(100),
- na.value= "gray80"
- )+
- guides(color = "none")+
- guides(fill = guide_colorbar(title = "Mean Threat",
- title.position = "top",
- direction = "horizontal",
- barwidth = 7,
- barheight = 1))+
- theme_void()+
- theme(
- #legend.position = c(0.1, 0.21),
- legend.ticks = element_blank(),
- legend.title = element_text(face = "bold"),
- legend.text = element_text(size = 11)
- )
-
-return(threat_map)
-
-}
-
-subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, subcat_pollution, subcat_climate, proj, hybas_habitat_types){
-
+general_threat_map <- function(in_dat, threat_category, threat_pal, hybas_habitat_types, proj){
filtered_df <- in_dat |>
left_join(hybas_habitat_types) |>
st_as_sf() |>
@@ -65,22 +8,10 @@ subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, s
proj_df <- st_transform(filtered_df, crs = st_crs(proj))
- if(threat_category %in% subcat_habitat){
- pal <- threat_pal$Habitat_pal
- } else if(threat_category %in% subcat_pollution){
- pal <- threat_pal$Pollution_pal
- } else if(threat_category == "Overfishing"){
- pal <- threat_pal$Exploitation_pal
- } else if(threat_category == "Invasive non-native species"){
- pal <- threat_pal$Invasive_pal
- } else if(threat_category %in% subcat_climate){
- pal <- threat_pal$Climate_pal
- }
-
threat_map <- ggplot()+
geom_sf(data = proj_df, aes(geometry = Shape, fill = MeanWeightedThreatMetric, color = MeanWeightedThreatMetric))+
scale_fill_gradientn(
- colors = colorRampPalette(c(rev(unlist(pal))))(100),
+ colors = colorRampPalette(c(rev(unlist(threat_pal))))(100),
limits = c(0, max(proj_df$MeanWeightedThreatMetric, na.rm = T)),
na.value = "gray80",
breaks = c(0 + max(proj_df$MeanWeightedThreatMetric, na.rm = T)/10,
@@ -89,7 +20,7 @@ subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, s
labels = c("Lower", "Higher")
)+
scale_color_gradientn(
- colors = colorRampPalette(c(rev(unlist(pal))))(100),
+ colors = colorRampPalette(c(rev(unlist(threat_pal))))(100),
na.value= "gray80"
)+
guides(color = "none")+
@@ -107,12 +38,53 @@ subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, s
)
return(threat_map)
+}
+
+threat_map <- function(in_dat, threat_category, threat_pal, hybas_habitat_types, proj){
+
+ if(threat_category == "Habitat"){
+ pal <- threat_pal$Habitat_pal
+ } else if(threat_category == "Pollution"){
+ pal <- threat_pal$Pollution_pal
+ } else if(threat_category == "Exploitation"){
+ pal <- threat_pal$Exploitation_pal
+ } else if(threat_category == "Invasive species"){
+ pal <- threat_pal$Invasive_pal
+ } else if(threat_category == "Climate and weather"){
+ pal <- threat_pal$Climate_pal
+ }
+ final_plot <- general_threat_map(in_dat = in_dat,
+ threat_category = threat_category,
+ threat_pal = pal,
+ hybas_habitat_types = hybas_habitat_types,
+ proj = proj)
+
}
-# in_dat = p2_mean_weighted_threats, legend_png = p3_legend_png, threat_category = threat_cat
-## note about out_file - need to find a way to save the cowplot version of the legend without crowding the images folder
-## maybe by saving the initial legend png in the findex out folder and then saving
-## the cowplot version to the earth-in-flux parent directory "src/assets/images/" folder
+
+subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, subcat_pollution, subcat_climate, proj, hybas_habitat_types){
+
+ # establish palette
+ if(threat_category %in% subcat_habitat){
+ pal <- threat_pal$Habitat_pal
+ } else if(threat_category %in% subcat_pollution){
+ pal <- threat_pal$Pollution_pal
+ } else if(threat_category == "Overfishing"){
+ pal <- threat_pal$Exploitation_pal
+ } else if(threat_category == "Invasive non-native species"){
+ pal <- threat_pal$Invasive_pal
+ } else if(threat_category %in% subcat_climate){
+ pal <- threat_pal$Climate_pal
+ }
+
+ final_plot <- general_threat_map(in_dat = in_dat,
+ threat_category = threat_category,
+ threat_pal = pal,
+ hybas_habitat_types = hybas_habitat_types,
+ proj = proj)
+
+}
+
cowplot_legend <- function(in_dat, legend_png, threat_category, out_file){
threat_df <- in_dat |>
@@ -170,4 +142,91 @@ cowplot_legend <- function(in_dat, legend_png, threat_category, out_file){
size = 9)
#429x176
ggsave(out_file, final_legend, height = 176, width = 429, units = "px", dpi = 300, bg = "transparent")
-}
\ No newline at end of file
+}
+
+# plot = final_plot, in_dat = p2_mean_weighted_threats
+save_legend <- function(type, plot, threat_category, subcat_habitat, subcat_pollution, subcat_climate, in_dat){
+
+ if(type == "threat"){
+
+ plot_legend <- get_plot_component(plot, "guide-box-right", return_all = T)
+
+ out_file <- paste0("out/", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+
+ ggsave(out_file,
+ plot_legend, dpi = 300, bg = "transparent")
+ knitr::plot_crop(out_file)
+
+ out_file_final <- paste0("../src/assets/images/", str_replace_all(threat_category, " ", "_"), "_legend.png")
+
+ cowplot_legend(in_dat = in_dat, legend_png = out_file, threat_category = threat_category, out_file = out_file_final)
+
+ return(out_file_final)
+
+ } else if(type == "subThreat"){
+
+ plot_legend <- get_plot_component(plot, "guide-box-right", return_all = T)
+
+ if(threat_category %in% subcat_habitat){
+ out_file <- paste0("out/H_", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ } else if(threat_category %in% subcat_pollution){
+ out_file <- paste0("out/P_", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ } else if(threat_category == "Overfishing"){
+ out_file <- paste0("out/E_", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ } else if(threat_category == "Invasive non-native species"){
+ out_file <- paste0("out/IS_", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ } else if(threat_category %in% subcat_climate){
+ out_file <- paste0("out/CW_", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ }
+
+ ggsave(out_file,
+ plot_legend, dpi = 300, bg = "transparent")
+ knitr::plot_crop(out_file)
+
+ if(threat_category %in% subcat_habitat){
+ out_file_final <- paste0("../src/assets/images/H_", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ } else if(threat_category %in% subcat_pollution){
+ out_file_final <- paste0("../src/assets/images/P_", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ } else if(threat_category == "Overfishing"){
+ out_file_final <- paste0("../src/assets/images/E_", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ } else if(threat_category == "Invasive non-native species"){
+ out_file_final <- paste0("../src/assets/images/IS_", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ } else if(threat_category %in% subcat_climate){
+ out_file_final <- paste0("../src/assets/images/CW_", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ }
+
+ cowplot_legend(in_dat = in_dat, legend_png = out_file, threat_category = threat_category, out_file = out_file_final)
+
+ return(out_file_final)
+
+ }
+}
+
+save_map <- function(type, plot, threat_category, subcat_habitat, subcat_pollution, subcat_climate){
+
+ if(type == "threat"){
+
+ out_file <- paste0("../src/assets/images/", str_replace_all(threat_category, " ", "_"), "_map.png")
+
+ ggsave(out_file,
+ plot, height = 6, width = 10, dpi = 300)
+
+ } else if(type == "subThreat"){
+
+ if(threat_category %in% subcat_habitat){
+ out_file <- paste0("../src/assets/images/H_", str_replace_all(threat_category, " ", "_"), "_map.png")
+ } else if(threat_category %in% subcat_pollution){
+ out_file <- paste0("../src/assets/images/P_", str_replace_all(threat_category, " ", "_"), "_map.png")
+ } else if(threat_category == "Overfishing"){
+ out_file <- paste0("../src/assets/images/E_", str_replace_all(threat_category, " ", "_"), "_map.png")
+ } else if(threat_category == "Invasive non-native species"){
+ out_file <- paste0("../src/assets/images/IS_", str_replace_all(threat_category, " ", "_"), "_map.png")
+ } else if(threat_category %in% subcat_climate){
+ out_file <- paste0("../src/assets/images/CW_", str_replace_all(threat_category, " ", "_"), "_map.png")
+ }
+
+ ggsave(out_file,
+ plot, height = 6, width = 10, dpi = 300)
+
+ }
+}