From 7776214eed33f7208e94f7fe58df153692152838 Mon Sep 17 00:00:00 2001
From: Kaysa Vaarre-Lamoureux <kvaarre-lamoureux@usgs.gov>
Date: Wed, 12 Feb 2025 16:08:23 -0500
Subject: [PATCH] add file names and palettes to viz_config target
---
findex/_targets.R | 95 +++++++++++++++++++++++++++--------------
findex/src/plot_utils.R | 89 +++++++++++---------------------------
2 files changed, 89 insertions(+), 95 deletions(-)
diff --git a/findex/_targets.R b/findex/_targets.R
index 81e686d..f39c355 100644
--- a/findex/_targets.R
+++ b/findex/_targets.R
@@ -129,44 +129,78 @@ p2 <- list(
filter(MajorCat == "Climate and weather") |>
pull(ThreatCategory) |>
unique()
+ ),
+ tar_target(p2_viz_config,
+ {
+ p2_mean_weighted_subThreats |>
+ select(MajorCat, ThreatCategory) |>
+ mutate(
+ # map color ramp
+ pal = case_when(
+ MajorCat == "Habitat" ~ list(c("#7A562B", "#C7985F", "#E1C8AA")),
+ MajorCat == "Exploitation" ~ list(c("#B74F49", "#E2B8B6")),
+ MajorCat == "Invasive species" ~ list(c("#4E6D6E", "#C9D8D9")),
+ MajorCat == "Pollution" ~ list(c("#002D5E", "#B2C0CE")),
+ MajorCat == "Climate and weather" ~ list(c("#835192", "#DDCCE2"))
+ ),
+ # legend and map file name template strings
+ threat_legend_raw = "out/%s_legend_raw.png",
+ threat_legend = "../src/assets/images/%s_legend.png",
+ threat_map = "../src/assets/images/%s_map.png",
+ subThreat_legend_raw = case_when(
+ MajorCat %in% "Habitat" ~ "out/H_%s_legend_raw.png",
+ MajorCat %in% "Exploitation" ~ "out/E_%s_legend_raw.png",
+ MajorCat %in% "Invasive species" ~ "out/IS_%s_legend_raw.png",
+ MajorCat %in% "Pollution" ~ "out/P_%s_legend_raw.png",
+ MajorCat %in% "Climate and weather" ~ "out/CW_%s_legend_raw.png"
+ ),
+ subThreat_legend = case_when(
+ MajorCat %in% "Habitat" ~ "../src/assets/images/H_%s_legend.png",
+ MajorCat %in% "Exploitation" ~ "../src/assets/images/E_%s_legend.png",
+ MajorCat %in% "Invasive species" ~ "../src/assets/images/IS_%s_legend.png",
+ MajorCat %in% "Pollution" ~ "../src/assets/images/P_%s_legend.png",
+ MajorCat %in% "Climate and weather" ~ "../src/assets/images/CW_%s_legend.png"
+ ),
+ subThreat_map = case_when(
+ MajorCat %in% "Habitat" ~ "../src/assets/images/H_%s_map.png",
+ MajorCat %in% "Exploitation" ~ "../src/assets/images/E_%s_map.png",
+ MajorCat %in% "Invasive species" ~ "../src/assets/images/IS_%s_map.png",
+ MajorCat %in% "Pollution" ~ "../src/assets/images/P_%s_map.png",
+ MajorCat %in% "Climate and weather" ~ "../src/assets/images/CW_%s_map.png"
+ )
+ )
+ }
)
)
p3 <- list(
- tar_target(p3_color_pal,
- tibble(
- Habitat_pal = list(c("#7A562B", "#C7985F", "#E1C8AA")), #A07138
- Pollution_pal = list(c("#002D5E", "#B2C0CE")),
- Exploitation_pal = list(c("#B74F49", "#E2B8B6")),
- Invasive_pal = list(c("#4E6D6E", "#C9D8D9")),
- Climate_pal = list(c("#835192", "#DDCCE2")) #9D6AAC
- )),
tar_target(
p3_threat_map_png,
{
final_plot <- threat_map(in_dat = p2_mean_weighted_threats,
threat_category = p2_threat_categories,
- threat_pal = p3_color_pal,
+ threat_pal = p2_viz_config,
hybas_habitat_types = p2_hybas_habitat_types_sf,
proj = p1_proj) +
theme(legend.position = "none")
save_map(type = "threat", plot = final_plot,
- threat_category = p2_threat_categories,
- subcat_habitat = NA,
- subcat_pollution = NA,
- subcat_climate = NA
- )
+ threat_category = p2_threat_categories,
+ subcat_habitat = NA,
+ subcat_pollution = NA,
+ subcat_climate = NA,
+ config_df = p2_viz_config
+ )
},
format = "file",
pattern = p2_threat_categories
),
- tar_target( # will turn this into a function
+ tar_target(
p3_legend_png,
{
final_plot <- threat_map(in_dat = p2_mean_weighted_threats,
threat_category = p2_threat_categories,
- threat_pal = p3_color_pal,
+ threat_pal = p2_viz_config,
proj = p1_proj,
hybas_habitat_types = p2_hybas_habitat_types_sf)
@@ -175,7 +209,8 @@ p3 <- list(
subcat_habitat = NA,
subcat_pollution = NA,
subcat_climate = NA,
- in_dat = p2_mean_weighted_threats)
+ in_dat = p2_mean_weighted_threats,
+ config_df = p2_viz_config)
},
pattern = p2_threat_categories
),
@@ -184,32 +219,27 @@ p3 <- list(
{
final_plot <- subThreat_map(in_dat = p2_mean_weighted_subThreats,
threat_category = p2_threat_subcategories,
- subcat_habitat = p2_habitat_subthreats,
- subcat_pollution = p2_pollution_subthreats,
- subcat_climate = p2_climate_subthreats,
- threat_pal = p3_color_pal,
+ threat_pal = p2_viz_config,
proj = p1_proj,
hybas_habitat_types = p2_hybas_habitat_types_sf) +
theme(legend.position = "none")
- 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)
+ save_map(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,
+ config_df = p2_viz_config)
},
format = "file",
pattern = p2_threat_subcategories
),
- tar_target( # will turn this into a function
+ tar_target(
p3_sub_threat_legend_png,
{
final_plot <- subThreat_map(in_dat = p2_mean_weighted_subThreats,
threat_category = p2_threat_subcategories,
- subcat_habitat = p2_habitat_subthreats,
- subcat_pollution = p2_pollution_subthreats,
- subcat_climate = p2_climate_subthreats,
- threat_pal = p3_color_pal,
+ threat_pal = p2_viz_config,
proj = p1_proj,
hybas_habitat_types = p2_hybas_habitat_types_sf)
@@ -218,7 +248,8 @@ p3 <- list(
subcat_habitat = p2_habitat_subthreats,
subcat_pollution = p2_pollution_subthreats,
subcat_climate = p2_climate_subthreats,
- in_dat = p2_mean_weighted_subThreats)
+ in_dat = p2_mean_weighted_subThreats,
+ config_df = p2_viz_config)
},
format = "file",
pattern = p2_threat_subcategories
diff --git a/findex/src/plot_utils.R b/findex/src/plot_utils.R
index 187a58e..c0944a1 100644
--- a/findex/src/plot_utils.R
+++ b/findex/src/plot_utils.R
@@ -42,17 +42,10 @@ general_threat_map <- function(in_dat, threat_category, threat_pal, hybas_habita
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$Climate_pal
- }
+ pal <- threat_pal |>
+ filter(MajorCat == threat_category) |>
+ select(pal) |>
+ unique()
final_plot <- general_threat_map(in_dat = in_dat,
threat_category = threat_category,
@@ -62,20 +55,12 @@ threat_map <- function(in_dat, threat_category, threat_pal, hybas_habitat_types,
}
-subThreat_map <- function(in_dat, threat_category, threat_pal, subcat_habitat, subcat_pollution, subcat_climate, proj, hybas_habitat_types){
-
- # establish palette
- if(threat_category %in% subcat_habitat){
- pal <- threat_pal$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
- }
+subThreat_map <- function(in_dat, threat_category, threat_pal, proj, hybas_habitat_types){
+
+ pal <- threat_pal |>
+ filter(ThreatCategory == threat_category) |>
+ select(pal) |>
+ unique()
final_plot <- general_threat_map(in_dat = in_dat,
threat_category = threat_category,
@@ -145,55 +130,39 @@ cowplot_legend <- function(in_dat, legend_png, threat_category, out_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){
+save_legend <- function(type, plot, threat_category, subcat_habitat, subcat_pollution, subcat_climate, in_dat, config_df){
if(type == "threat"){
+ name_conv <- config_df |>
+ filter(MajorCat == threat_category)
plot_legend <- get_plot_component(plot, "guide-box-right", return_all = T)
- out_file <- paste0("out/", str_replace_all(threat_category, " ", "_"), "_legend_raw.png")
+ out_file <- sprintf(unique(name_conv$threat_legend_raw), str_replace_all(threat_category, " ", "_"))
ggsave(out_file,
plot_legend, dpi = 300, bg = "transparent")
knitr::plot_crop(out_file)
- out_file_final <- paste0("../src/assets/images/", str_replace_all(threat_category, " ", "_"), "_legend.png")
+ out_file_final <- sprintf(unique(name_conv$threat_legend), str_replace_all(threat_category, " ", "_"))
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"){
+ name_conv <- config_df |>
+ filter(ThreatCategory == threat_category)
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")
- }
+ out_file <- sprintf(unique(name_conv$subThreat_legend_raw), str_replace_all(threat_category, " ", "_"))
ggsave(out_file,
plot_legend, dpi = 300, bg = "transparent")
knitr::plot_crop(out_file)
- if(threat_category %in% subcat_habitat){
- out_file_final <- paste0("../src/assets/images/H_", str_replace_all(threat_category, " ", "_"), "_legend.png")
- } else if(threat_category %in% subcat_pollution){
- out_file_final <- paste0("../src/assets/images/P_", str_replace_all(threat_category, " ", "_"), "_legend.png")
- } else if(threat_category == "Overfishing"){
- out_file_final <- paste0("../src/assets/images/E_", str_replace_all(threat_category, " ", "_"), "_legend.png")
- } else if(threat_category == "Invasive non-native species"){
- out_file_final <- paste0("../src/assets/images/IS_", str_replace_all(threat_category, " ", "_"), "_legend.png")
- } else if(threat_category %in% subcat_climate){
- out_file_final <- paste0("../src/assets/images/CW_", str_replace_all(threat_category, " ", "_"), "_legend.png")
- }
+ out_file_final <- sprintf(unique(name_conv$subThreat_legend), str_replace_all(threat_category, " ", "_"))
cowplot_legend(in_dat = in_dat, legend_png = out_file, threat_category = threat_category, out_file = out_file_final)
@@ -202,28 +171,22 @@ save_legend <- function(type, plot, threat_category, subcat_habitat, subcat_poll
}
}
-save_map <- function(type, plot, threat_category, subcat_habitat, subcat_pollution, subcat_climate){
+save_map <- function(type, plot, threat_category, subcat_habitat, subcat_pollution, subcat_climate, config_df){
if(type == "threat"){
+ name_conv <- config_df |>
+ filter(MajorCat == threat_category)
- out_file <- paste0("../src/assets/images/", str_replace_all(threat_category, " ", "_"), "_map.png")
+ out_file <- sprintf(unique(name_conv$threat_map), str_replace_all(threat_category, " ", "_"))
ggsave(out_file,
plot, height = 6, width = 10, dpi = 300)
} else if(type == "subThreat"){
+ name_conv <- config_df |>
+ filter(ThreatCategory == threat_category)
- if(threat_category %in% subcat_habitat){
- out_file <- paste0("../src/assets/images/H_", str_replace_all(threat_category, " ", "_"), "_map.png")
- } else if(threat_category %in% subcat_pollution){
- out_file <- paste0("../src/assets/images/P_", str_replace_all(threat_category, " ", "_"), "_map.png")
- } else if(threat_category == "Overfishing"){
- out_file <- paste0("../src/assets/images/E_", str_replace_all(threat_category, " ", "_"), "_map.png")
- } else if(threat_category == "Invasive non-native species"){
- out_file <- paste0("../src/assets/images/IS_", str_replace_all(threat_category, " ", "_"), "_map.png")
- } else if(threat_category %in% subcat_climate){
- out_file <- paste0("../src/assets/images/CW_", str_replace_all(threat_category, " ", "_"), "_map.png")
- }
+ out_file <- sprintf(unique(name_conv$subThreat_map), str_replace_all(threat_category, " ", "_"))
ggsave(out_file,
plot, height = 6, width = 10, dpi = 300)
--
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