MOCHA: exploring seasonal datasets
The case of polar seas: data from three indepedent studies
Studies S3 (spring) and S19 (summer) were in the Ross Sea, Antartica. Study S17 (early-autumn) was in the Beaufort Sea, Canada Basin.
Load libraries:
library(ggplot2)
library(dplyr)Import the data, filter polar studies and separate by sampling depth.
data <- read.table('field_data.txt', header = T)
data$alatitude <- abs(data$latitude)
# Quantifying the relative proportion of mixotrophs to total phagotrophs:
data$pmixophago <- 100 * data$mnf/(data$mnf + data$hnf)
# Quantifying the relative proportion of mixotrophs to total phagotrophs:
data$pmixophoto <- 100 * data$mnf/(data$mnf + data$anf)
# Weighting to get "community mixotrophy"
tot <- data$mnf + data$anf + data$hnf
data$phot <- 0.5 * (data$mnf/tot) + 1.0 * (data$anf/tot)
data$phag <- 0.5 * (data$mnf/tot) + 1.0 * (data$hnf/tot)
data_polar <- data %>%
filter(study == "S3" | study == "S17" | study == "S19")
data_polar$season <- factor(data_polar$season, levels = c("spring", "summer", "early-autumn"))
data_surface <- data_polar %>%
filter(depth == "surface")
data_dcm <- data_polar %>%
filter(depth == "DCM")
data_surface %>%
group_by(season) %>%
summarise_at(vars(mnpp:npratio, bacteria:mnf, chla:PAR), mean, na.rm = TRUE)## # A tibble: 3 x 13
## season mnpp vnpp nitrate phosphate npratio bacteria anf hnf mnf chla
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 spring 0.532 0.104 28.8 1.96 14.7 5513077. 2531. 555. 93.5 1.55
## 2 summer 0.683 0.104 20.6 1.39 15.1 368769. 1405. 353. 191. 1.87
## 3 early~ 0.215 0.132 0.538 0.952 0.485 214700 44.6 106. 10.9 0.252
## # ... with 2 more variables: temperature <dbl>, PAR <dbl>data_dcm %>%
group_by(season) %>%
summarise_at(vars(mnpp:npratio, bacteria:mnf, chla:PAR), mean, na.rm = TRUE)## # A tibble: 2 x 13
## season mnpp vnpp nitrate phosphate npratio bacteria anf hnf mnf chla
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 summer 0.683 0.104 25.0 1.64 15.3 440538. 1213. 342. 192. 1.87
## 2 early~ 0.215 0.132 5.12 1.41 3.42 179900 68.6 86.4 10.5 0.3
## # ... with 2 more variables: temperature <dbl>, PAR <dbl>Plot environmental conditions in the polar seas
# Settings for plots
mytheme <- theme(panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
panel.background = element_rect(colour = "black", fill = "white", size=1),
axis.text=element_text(size=16, colour ="black"),
axis.title=element_text(size=18, colour ="black"),
axis.ticks.length = unit(.25, "cm"),
plot.margin = unit(c(1, 1.5, 0.5, 0.5), "lines"),
legend.position = 'right',
#legend.title = element_blank(),
legend.text = element_text(size=16, colour ="black"),
legend.title = element_text(size=16, colour ="black"),
plot.title = element_text(hjust = -0.28, face = "bold", size = 25),
strip.background = element_rect(colour="black", fill="white"),
strip.text = element_text(size = 16)
)
ggplot(data = data_surface, aes(x = season, y = log(bacteria + 1))) +
geom_boxplot() +
ylab("Bacteria (cells/mL) - surface") +
mytheme
ggplot(data = data_surface, aes(x = season, y = PAR)) +
geom_boxplot() +
ylab("PAR (mol photons/m2/day) - surface") +
mytheme
ggplot(data = data_surface, aes(x = season, y = nitrate)) +
geom_boxplot() +
ylab("Nitrate (uM) - surface") +
mytheme
Plotting nanoflagellate data and community mixotrophy (Polar Seas)
ggplot(data = data_surface, aes(x = season, y = mnf)) +
geom_boxplot() +
ylab("MNF (cells/mL)") +
mytheme
ggplot(data = data_surface, aes(x = season, y = anf)) +
geom_boxplot() +
ylab("ANF (cells/mL)") +
mytheme
ggplot(data = data_surface, aes(x = season, y = hnf)) +
geom_boxplot() +
ylab("HNF (cells/mL)") +
mytheme
ggplot(data = data_surface, aes(x = season, y = pmixophago)) +
geom_boxplot() +
ylab("MNF:(MNF + HNF)") +
mytheme
ggplot(data = data_surface, aes(x = season, y = pmixophoto)) +
geom_boxplot() +
ylab("MNF:(MNF + ANF)") +
mytheme
ggplot(data = data_surface, aes(x = season, y = phot)) +
geom_boxplot() +
ylab("Community phototrophy (surface)") +
mytheme
ggplot(data = data_dcm, aes(x = season, y = phot)) +
geom_boxplot() +
ylab("Community phototrophy (DCM)") +
mytheme
ggplot(data = data_polar, aes(x = season, y = phot)) +
geom_boxplot() +
ylab("Community phototrophy (all depths)") +
mytheme
The case of oligotrophic seas: data from two indepedent studies
Studies S1 (spring and summer) and S2 (autumn, summer) were in the Sargasso Sea.
data_olig <- data %>%
filter(study == "S1" | study == "S2")
data_olig$season <- factor(data_olig$season, levels = c("spring", "summer", "autumn"))
data_surface <- data_olig %>%
filter(depth == "surface")
data_dcm <- data_olig %>%
filter(depth == "DCM")
data_surface %>%
group_by(season) %>%
summarise_at(vars(mnpp:npratio, bacteria:mnf, chla:PAR), mean, na.rm = TRUE)## # A tibble: 3 x 13
## season mnpp vnpp nitrate phosphate npratio bacteria anf hnf mnf chla
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 spring 0.5 0.0129 0.005 0.1 0.05 390000 175 974 22 0.05
## 2 summer 0.538 0.0354 0.198 0.0549 3.60 545000 1634 1358. 192. 1.1
## 3 autumn 0.865 0.0747 2.95 0.654 4.51 2225000 4510 1305 135 3.47
## # ... with 2 more variables: temperature <dbl>, PAR <dbl>data_dcm %>%
group_by(season) %>%
summarise_at(vars(mnpp:npratio, bacteria:mnf, chla:PAR), mean, na.rm = TRUE)## # A tibble: 2 x 13
## season mnpp vnpp nitrate phosphate npratio bacteria anf hnf mnf
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 spring 0.5 0.0129 1.06 0.345 3.06 283500 1172. 809 1.75
## 2 summer 0.285 0.0129 0.18 0.06 3 126833. 706. 275. 18.2
## # ... with 3 more variables: chla <dbl>, temperature <dbl>, PAR <dbl>Plot environmental conditions in the oligotrophic seas
ggplot(data = data_olig, aes(x = season, y = log(bacteria + 1))) +
geom_boxplot() +
ylab("Bacteria (cells/mL)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = PAR)) +
geom_boxplot() +
ylab("PAR (mol photons/m2/day)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = nitrate)) +
geom_boxplot() +
ylab("Nitrate (uM)") +
mytheme
Plotting nanoflagellate data and community mixotrophy (Oligotrophic Seas)
The overall abundance of ANF, MNF and HNF decreases from autumn to summer. The propotion of MNF to HNF is higher during autumn and lower during spring, similar to the proportion of MNF to ANF. Overall community phototrophy decreases throughout the seasonal cycle.
ggplot(data = data_olig, aes(x = season, y = mnf)) +
geom_boxplot() +
ylab("MNF (cells/mL)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = anf)) +
geom_boxplot() +
ylab("ANF (cells/mL)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = hnf)) +
geom_boxplot() +
ylab("HNF (cells/mL)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = pmixophago)) +
geom_boxplot() +
ylab("MNF:(MNF+HNF)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = pmixophoto)) +
geom_boxplot() +
ylab("MNF:(MNF+ANF)") +
mytheme
ggplot(data = data_olig, aes(x = season, y = phot)) +
geom_boxplot() +
ylab("Community phototrophy") +
mytheme
