Environmental metadata

Import metadata & combine

library(tidyverse); library(patchwork)

tmp_all_metadata <- read.csv("input-data/All_metadata.csv")
# colnames(tmp_all_metadata)
# unique(tmp_all_metadata$Site)
# View(tmp_all_metadata)
july <- read.delim("input-data/flor_env_ALOHAJuly_SPOT.txt")
march <- read.delim("input-data/flour_ALOHAMarch.txt")

# head(july)
# head(march)
fluor <- july %>% 
  left_join(march) %>% 
  pivot_longer(cols = SPOT:ALOHAMarch, names_to = "Site", values_to = "Fluor")

Joining with `by = join_by(Depth)`

# unique(fluor$Site)
metadata_all <- tmp_all_metadata %>% 
  filter((!Site == "ALOHA")) %>% 
  select(-X) %>% 
  left_join(fluor) %>% 
  pivot_longer(cols = Temp:Fluor, names_to = "VARIABLE", values_to = "VALUE")

Joining with `by = join_by(Site, Depth, Fluor)`

# head(metadata_all)
# unique(metadata_all$Site)

Figure aesthetics

site_order <- c("SPOT", "PortofLA", "Catalina", "ALOHAJuly", "ALOHAMarch")
site_label <- c("SPOT", "Port of LA", "Catalina", "ALOHA July", "ALOHA March")
site_color_fill <- c("#3288bd", "#8073ac", "#66bd63", "#e6f598", "#d53e4f")
site_color_fill_nopola <- c("#3288bd", "#66bd63", "#e6f598", "#d53e4f")

Isolate specific depths, add a label

spot<-c(1,150,885)
spotsite<-c("SPOT", "Catalina", "PortofLA")
aloha<-c(1,120,150,1000)

metadata_pt_depth <- metadata_all %>% 
  filter(Site %in% spotsite & Depth %in% spot | grepl("ALOHA", Site) & Depth %in% aloha) %>% 
  add_column(Label = "discrete") %>% 
  mutate(VAR_ORDER = factor(VARIABLE, levels = c("Temp", "Fluor", "Sal", "Oxy"), labels = c("Temperature", "Chlorophyll", "Salinity", "Oxygen"))) %>% 
  mutate(SITE_ORDER = factor(Site, levels = site_order, labels = site_label))
# unique(metadata_all$Site)

allenv <- metadata_all %>% 
  mutate(VAR_ORDER = factor(VARIABLE, levels = c("Temp", "Fluor", "Sal", "Oxy"), labels = c("Temperature", "Chlorophyll", "Salinity", "Oxygen"))) %>% 
  mutate(SITE_ORDER = factor(Site, levels = site_order, labels = site_label)) %>% 
  arrange(Depth) %>% 
  ggplot(aes(y = Depth, x = VALUE)) +
  geom_hline(yintercept = 0, alpha = 0.3) +
  geom_path(size = 1, aes(color = SITE_ORDER)) +
  geom_point(data = metadata_pt_depth, size = 2, aes(y = Depth, x = VALUE, fill = SITE_ORDER, shape = SITE_ORDER)) +
    scale_shape_manual(values = c(21, 22, 23, 24, 25)) +
    scale_fill_manual(values = site_color_fill) +
    scale_color_manual(values = site_color_fill) +
  scale_y_reverse() +
  facet_grid(. ~ VAR_ORDER, scales = "free", switch = "both") +
  theme_linedraw() +
  labs(x = "", y = "Depth (m)") +
  theme(strip.background = element_blank(),
        strip.placement = "outside",
        strip.text = element_text(color = "black"),
        legend.title = element_blank())

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

allenv

Warning: Removed 2 rows containing missing values (`geom_path()`).

no_pola <- metadata_all %>% 
  mutate(VAR_ORDER = factor(VARIABLE, levels = c("Temp", "Fluor", "Sal", "Oxy"), labels = c("Temperature", "Chlorophyll", "Salinity", "Oxygen"))) %>% 
  mutate(SITE_ORDER = factor(Site, levels = site_order, labels = site_label)) %>% 
  arrange(Depth) %>% 
  filter(Site != "PortofLA") %>% 
  ggplot(aes(y = Depth, x = VALUE)) +
  geom_hline(yintercept = 0, alpha = 0.3) +
  geom_path(size = 1, aes(color = SITE_ORDER)) +
  geom_point(data = (metadata_pt_depth %>% filter(Site != "PortofLA")), size = 2, aes(y = Depth, x = VALUE, fill = SITE_ORDER, shape = SITE_ORDER)) +
    scale_shape_manual(values = c(21, 22, 23, 24, 25)) +
    scale_fill_manual(values = site_color_fill_nopola) +
    scale_color_manual(values = site_color_fill_nopola) +
  scale_y_reverse() +
  facet_grid(. ~ VAR_ORDER, scales = "free", switch = "both") +
  theme_linedraw() +
  labs(x = "", y = "Depth (m)") +
  theme(strip.background = element_blank(),
        strip.placement = "outside",
        strip.text = element_text(color = "black"),
        legend.title = element_blank())

no_pola

Warning: Removed 2 rows containing missing values (`geom_path()`).

# svg("figs/water-col.svg", w = 8, h = 7)
allenv + no_pola + patchwork::plot_layout(ncol = 1)

Warning: Removed 2 rows containing missing values (`geom_path()`).
Removed 2 rows containing missing values (`geom_path()`).

# dev.off()

# Requires manual modification of chlorophyll with Port of LA sample