Update map scripts using code from EMP maps to make Illustrator expor…

…t easier.

FASTR_map.R

@@ -48,7 +48,7 @@ locations_text<-tibble(Location=c("Freeport", "Antioch", "Rio Vista", "Cache Slo
 
 
 p<-ggplot()+
-  geom_sf(data=yolo, color=NA, fill="gray80", alpha=0.5)+
+  geom_sf(data=yolo, color=NA, fill="gray80")+
   geom_sf(data=base, fill="slategray3", color="slategray4")+
   geom_sf(data=locations_points)+
   geom_sf(data=stations, aes(fill=Region), shape=21, color="black", size=3)+
@@ -60,6 +60,8 @@ p
 ggsave(here("manuscript_synthesis","plots","FASTR_MS_map.pdf"), 
        plot=p, 
        device="pdf", 
+       scale=1.0,
        width=8, 
        height=8, 
-       units = "in")
+       units = "in",
+       dpi="print")

manuscript_synthesis/FASTR-map-pub.R

@@ -0,0 +1,101 @@
+## Generate map of FASTR sampling locations
+## 6/3/2024
+
+# Load required libraries ------------------------------------------------------
+suppressWarnings(suppressMessages(library(tidyverse)))
+suppressWarnings(suppressMessages(library(deltamapr)))
+suppressWarnings(suppressMessages(library(sf)))
+suppressWarnings(suppressMessages(library(ggrepel)))
+suppressWarnings(suppressMessages(library(ggspatial)))
+suppressWarnings(suppressMessages(library(maps)))
+suppressWarnings(suppressMessages(library(here)))
+
+# Set plot themes and output ---------------------------------------------------
+plots <- here(file = here("manuscript_synthesis","plots"))
+
+# Read in FASTR station and city location data ---------------------------------
+
+# Import data about city locations
+CA <- map_data("world") %>% filter(subregion=="California")
+cities <- world.cities %>% filter(country.etc=="USA")
+
+# Import FASTR station data (Laura code)
+SubRegions<-deltamapr::R_EDSM_Subregions_Mahardja%>%
+  filter(Region!="South")%>%
+  filter(!SubRegion%in%c("Upper Napa River", "Lower Napa River", "San Pablo Bay", "San Francisco Bay"))
+
+yolo<-sf::st_read(here("manuscript_synthesis","data","Yolo Bypass Extent"))%>%
+  st_transform(crs=st_crs(SubRegions))%>%
+  st_union()
+
+add<-tibble(Latitude=c(37.9, 38.8), Longitude=c(-121.9, -121.2))%>%
+  st_as_sf(coords=c("Longitude", "Latitude"), crs=4326)%>%
+  st_transform(crs=st_crs(SubRegions))
+
+base<-deltamapr::WW_Watershed%>%
+  st_transform(crs=st_crs(SubRegions))%>%
+  st_crop(st_union(st_union(st_buffer(yolo, units::set_units(3000, "m")), SubRegions), add))%>%
+  filter(!HNAME%in%c("PUTAH CREEK", "LAKE BERRYESSA", "SOUTH FORK PUTAH CREEK", "LAKE CURRY", "UPPER SAN LEANDRO RESERVOIR", "BETHANY RESERVOIR", "LAKE CHABOT", "SAN FRANCISCO BAY"))%>%
+  st_union()
+
+stations<-tibble(Station=c("RCS", "RD22", "I80", "LIS", "STTD", "BL5", "LIB", "RYI", "RVB"),
+                 Region=c(rep("Upstream", 5), rep("Downstream", 4)),
+                 Latitude=c(38.793457, 38.676367, 38.573111, 38.474816, 38.353461, 38.274460, 38.242100, 38.213167, 38.159737),
+                 Longitude=c(-121.725447, 	-121.643972, -121.582958, -121.588584, -121.642975, -121.665652, -121.684900,-121.668591, -121.686355))%>%
+  st_as_sf(coords=c("Longitude", "Latitude"), crs=4326)%>%
+  mutate(Region=factor(Region, levels=c("Upstream", "Downstream")))
+
+locations_points<-tibble(Location=c( "Freeport", "Antioch"),
+                         Latitude=c(38.461562, 38.004094),
+                         Longitude=c(-121.499371, -121.805606))%>%
+  st_as_sf(coords=c("Longitude", "Latitude"), crs=4326)
+
+locations_text<-tibble(Location=c("Freeport", "Antioch", "Rio Vista", "Cache Slough", "Yolo Bypass", "Sacramento River"),
+                       Latitude=c(38.481562, 37.99, 38.155603, 38.36, 38.5, 38.51),
+                       Longitude=c(-121.419371, -121.805606, -121.77, -121.78, -121.7, -121.38))%>%
+  st_as_sf(coords=c("Longitude", "Latitude"), crs=4326)
+
+
+# Plot all stations maps together ----------------------------------------------
+theme_set(theme_bw())
+
+# Set the theme
+theme_update(
+  panel.grid.major = element_blank(),
+  panel.grid.minor = element_blank(),
+  plot.background = element_rect(fill = "white", colour = NA),
+  panel.background = element_rect(fill = "white", colour = NA),
+  panel.border = element_rect(fill = NA, colour = "black"),
+  strip.background = element_rect(fill = "gray", colour = "black"),
+  legend.position = "bottom",
+  legend.key = element_rect(fill = "white", colour = NA)
+)
+
+plot <- ggplot(WW_Delta) +
+  geom_sf(data=yolo, color=NA, fill="gray80")+
+  geom_sf(data=base, fill="slategray3", color="slategray4")+
+  geom_sf(data=locations_points)+
+  geom_sf_text(data=locations_text, aes(label=Location), lineheight = 1)+
+  geom_sf(fill = "lightblue") + 
+  geom_sf(data=stations, aes(fill=Region), shape=21, color="black", size=3)+
+  geom_sf_text(data=stations, aes(label=Station), nudge_x = 0.05)+
+  annotation_scale(location = "bl", 
+                   width_hint = 0.4, 
+                   unit_category = "imperial") +
+  scale_fill_manual(values=c("#E41A1C", "#377EB8")) +
+  ylim(38.0, 38.8) +
+  xlim(-122.2, -121.2)
+
+plot + labs(x = NULL,
+            y = NULL,
+            fill = NULL) +
+  guides(size = "none")
+
+ggsave(path=plots,
+       filename = "FASTR-stations-all.pdf", 
+       device = "pdf",
+       scale=1.0, 
+       units="in",
+       height=8,
+       width=8, 
+       dpi="print")