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R code for figures and analyses
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‎Figures&Code/Figure_2/Figure_2-MegAshleySES.R‎

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# Figure 2 in Meg/Ashley SES Manuscript
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# Environmental parameters from chemostats (pH, CO2, O2, Dissolved O2)
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# UPLOAD DATA----
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path = "/Users/abulseco/Dropbox/MBL_Postdoc/Experiments/2018_Pilot_SESProject/Microbial_Data/Downloads_from_VAMPS/JJV_MEG_Bv4v5"
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setwd("~/Dropbox/MBL_Postdoc/Experiments/2018_Pilot_SESProject/Microbial_Data/Downloads_from_VAMPS/JJV_MEG_Bv4v5")
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# Load necessary libraries
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library("ggplot2")
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library(patchwork)
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# This is a slightly different theme function from others
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pretty.theme <- function(){
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theme_bw()+
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theme(axis.text.x=element_text(size=14, color = "black", angle = 0, hjust = 1),
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axis.text.y=element_text(size=14, color = "black"),
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axis.title.x=element_text(size=20, color = "black"),
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axis.title.y=element_text(size=20, color = "black"),
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panel.grid.major.x=element_blank(),
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panel.grid.minor.x=element_blank(),
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panel.grid.minor.y=element_blank(),
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panel.grid.major.y=element_blank(),
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plot.margin = unit(c(0.5, 0.5, 0.5, 0.5), units = , "cm"),
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plot.title = element_text(size=20),
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legend.text = element_text(size=12, face="italic"),
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legend.title = element_blank(),
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legend.position="none")
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}
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theme.exp1 <- function(){
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theme_bw()+
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theme(axis.text.x=element_text(size=18, vjust=1, hjust=1, color = "black"),
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axis.text.y=element_text(size=18, color = "black"),
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axis.title.x=element_text(size=14, face="plain"),
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axis.title.y=element_text(size=14, face="plain"),
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panel.grid.major.x=element_blank(),
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panel.grid.minor.x=element_blank(),
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panel.grid.minor.y=element_blank(),
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panel.grid.major.y=element_blank(),
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plot.title = element_text(size=20, vjust=1, hjust=0.5),
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legend.text = element_text(size=12, face="italic"),
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legend.title = element_blank(),
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axis.title = element_blank())
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}
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# Read in the data (dissolved O2 had a different output)
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monitor_var <- read.csv("monitor_param_LONG.csv", header = T)
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str(monitor_var)
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dissolved_oxy <- read.csv("dissolved_oxygen.csv", header = T)
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# pH Plot
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#############################################################################
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#############################################################################
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ph_plot <- ggplot(monitor_var, group = chemostat_ID, aes(x = time, y = ph)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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# geom_vline(xintercept = 15.71, color = "black", linetype = "dashed") +
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# geom_vline(xintercept = 20.79, color = "black", linetype = "dashed") +
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# scale_fill_manual(values = c("#3399CC", "#003399", linetype = "dashed")) +
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scale_color_manual(values = c("black", "gray45", linetype = "dashed")) +
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# facet_wrap(chemostat_ID~.) +
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geom_line(size = 0.75, aes(linetype = chemostat_ID)) +
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pretty.theme() +
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theme(strip.background = element_blank(), # Overriding some of the original theme
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strip.text.x = element_blank(),
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axis.title.x=element_blank(),
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axis.title.y=element_blank(),
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legend.position = "none")
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ph_plot
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# CO2 Plot
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#############################################################################
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#############################################################################
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CO2_plot <- ggplot(monitor_var, group = chemostat_ID, aes(x = time, y = carbon_dio_perc)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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# geom_vline(xintercept = 15.71, color = "black", linetype = "dashed") +
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# geom_vline(xintercept = 20.79, color = "black", linetype = "dashed") +
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# scale_fill_manual(values = c("#3399CC", "#003399", linetype = "dashed")) +
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scale_color_manual(values = c("black", "gray45", linetype = "dashed")) +
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# facet_wrap(chemostat_ID~.) +
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geom_line(size = 0.75, aes(linetype = chemostat_ID)) +
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pretty.theme() +
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theme(strip.background = element_blank(),
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strip.text.x = element_blank(),
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axis.title.x=element_blank(),
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axis.text.x=element_blank(),
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axis.title.y=element_blank(),
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legend.position = "none")
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CO2_plot
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# O2 Plot
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#############################################################################
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#############################################################################
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O2_plot <- ggplot(monitor_var, group = chemostat_ID, aes(x = time, y = oxygen_perc)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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# geom_vline(xintercept = 15.71, color = "black", linetype = "dashed") +
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# geom_vline(xintercept = 20.79, color = "black", linetype = "dashed") +
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# scale_fill_manual(values = c("#3399CC", "#003399", linetype = "dashed")) +
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scale_color_manual(values = c("black", "gray45", linetype = "dashed")) +
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# facet_wrap(chemostat_ID~.) +
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geom_line(size = 0.75, aes(linetype = chemostat_ID)) +
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pretty.theme() +
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theme(strip.background = element_blank(),
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strip.text.x = element_blank(),
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axis.title.x=element_blank(),
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axis.text.x=element_blank(),
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axis.title.y=element_blank(),
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legend.position = "none")
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O2_plot
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# Dissolved O2 Plot
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#############################################################################
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#############################################################################
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diss_O2_plot <- ggplot(dissolved_oxy, group = chemostat_ID, aes(x = time, y = diss_o2)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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# geom_vline(xintercept = 15.71, color = "black", linetype = "dashed") +
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# geom_vline(xintercept = 20.79, color = "black", linetype = "dashed") +
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# scale_fill_manual(values = c("#3399CC", "#003399", linetype = "dashed")) +
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scale_color_manual(values = c("black", "gray45", linetype = "dashed")) +
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# facet_wrap(chemostat_ID~.) +
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geom_line(size = 0.75, aes(linetype = chemostat_ID)) +
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pretty.theme() +
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theme(strip.background = element_blank(),
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strip.text.x = element_blank(),
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axis.title.x=element_blank(),
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axis.text.x=element_blank(),
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axis.title.y=element_blank(),
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legend.position = "none")
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diss_O2_plot
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# Then using patchwork, connect all the plots
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# After exporting to PDF, use InkScape to add in timeline along the top
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# axes labels along the left of each plot, and legend for MC1 and MC2.
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pdf("Fig2.pdf")
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CO2_plot + O2_plot + diss_O2_plot + ph_plot + plot_layout(ncol = 1)
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dev.off()
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# CREATING A TIMELINE PLOT
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# FROM THIS AWESOME BLOG POST: https://benalexkeen.com/creating-a-timeline-graphic-using-r-and-ggplot2/
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#############################################################################
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#############################################################################
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# (But it is not being used in the figure)
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df <- read.csv("sampling_timeline_final.csv")
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status_levels <- c("A", "B", "C")
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status_colors <- c("#2B5B6C", "#E34F33", "#FFC87E")
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df$dilution_rate <- factor(df$dilution_rate, levels=status_levels, ordered=TRUE)
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# PLOT
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timeline_plot<-ggplot(df,aes(x=time,y=0, col=dilution_rate))
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# timeline_plot<-timeline_plot+labs(col="dilution_rate")
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timeline_plot<-timeline_plot+scale_color_manual(values=status_colors, labels=status_levels, drop = FALSE)
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timeline_plot<-timeline_plot+theme_classic()
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# Plot horizontal black line for timeline
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timeline_plot<-timeline_plot+geom_hline(yintercept=0,
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color = "black", size=0.3)
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# Plot scatter points at zero and date
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timeline_plot<-timeline_plot+geom_point(aes(y=0), size=2)
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# Don't show axes, appropriately position legend
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timeline_plot<-timeline_plot+theme(axis.line.y=element_blank(),
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axis.text.y=element_blank(),
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axis.title.x=element_blank(),
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axis.title.y=element_blank(),
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axis.ticks.y=element_blank(),
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axis.text.x =element_blank(),
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axis.ticks.x =element_blank(),
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axis.line.x =element_blank(),
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legend.title = element_blank(),
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legend.position="none"
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) + scale_x_continuous(limits=c(0, 25)) +
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scale_y_continuous(limits=c(-1,1))
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timeline_plot

‎Figures&Code/Figure_2/dissolved_oxygen.csv‎

Whitespace-only changes.

‎Figures&Code/Figure_2/monitor_param.csv‎

Whitespace-only changes.

‎Figures&Code/Figure_2/monitor_param_LONG.csv‎

Whitespace-only changes.

‎Figures&Code/Figure_2/sampling_timeline_final.csv‎

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sampling_timept,time,dilution_rate
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1,1.7,A
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2,6.82,A
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3,10.5,A
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4,15.46,A
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5,16.46,B
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6,17.13,B
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7,19.84,B
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8,21.47,B
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9,19.84,B
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10,21.47,C
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11,21.8,C
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12,22.39,C
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13,22.8,C
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14,23.55,C

‎Figures&Code/Figure_3/Figure_3-MegAshleySES.R‎

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# Figure 2 in Meg/Ashley SES Manuscript
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# Environmental parameters from chemostats
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# UPLOAD DATA----
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path = "/Users/abulseco/Dropbox/MBL_Postdoc/Experiments/2018_Pilot_SESProject/Microbial_Data/Downloads_from_VAMPS/JJV_MEG_Bv4v5"
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setwd("~/Dropbox/MBL_Postdoc/Experiments/2018_Pilot_SESProject/Microbial_Data/Downloads_from_VAMPS/JJV_MEG_Bv4v5")
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# Load necessary libraries
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library("ggplot2")
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library(patchwork)
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pretty.theme <- function(){
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theme_bw()+
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theme(axis.text.x=element_text(size=14, color = "black", angle = 0, hjust = 1),
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axis.text.y=element_text(size=14, color = "black"),
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axis.title.x=element_text(size=20, color = "black"),
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axis.title.y=element_text(size=20, color = "black"),
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panel.grid.major.x=element_blank(),
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panel.grid.minor.x=element_blank(),
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panel.grid.minor.y=element_blank(),
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panel.grid.major.y=element_blank(),
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plot.margin = unit(c(0.5, 0.5, 0.5, 0.5), units = , "cm"),
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plot.title = element_text(size=20),
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legend.text = element_text(size=12, face="italic"),
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legend.title = element_blank(),
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legend.position="none")
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}
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nuts_data <- read.csv("new_nutrients.csv", header = TRUE)
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nitrate_plot <- ggplot(nuts_data, aes(x = days_after, y = nitrate_conc)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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geom_point(aes(shape = chemostat_ID, color = chemostat_ID), size = 2) +
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geom_line(aes(color = chemostat_ID, linetype = chemostat_ID)) +
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labs(y = expression (""), x = "Days After Start") +
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scale_color_manual(values = c("black", "black")) +
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pretty.theme()
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nitrate_plot
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phosphate_plot <- ggplot(nuts_data, aes(x = days_after, y = phos_conc)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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geom_point(aes(shape = chemostat_ID, color = chemostat_ID), size = 2) +
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geom_line(aes(color = chemostat_ID, linetype = chemostat_ID)) +
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labs(y = expression (""), x = "Days After Start") +
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scale_color_manual(values = c("black", "black")) +
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pretty.theme()
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phosphate_plot
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ammonium_plot <- ggplot(nuts_data, aes(x = days_after, y = ammonium_con)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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geom_point(aes(shape = chemostat_ID, color = chemostat_ID), size = 2) +
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geom_line(aes(color = chemostat_ID, linetype = chemostat_ID)) +
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labs(y = expression (""), x = "Days After Start") +
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scale_color_manual(values = c("black", "black")) +
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pretty.theme()
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ammonium_plot
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DOC_plot <- ggplot(nuts_data, aes(x = days_after, y = doc_conc_mmol)) +
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annotate("rect", fill = "#2B5B6C", alpha = 0.4,
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xmin = 0, xmax = 15.71,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#E34F33", alpha = 0.4,
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xmin = 15.71, xmax = 20.79,
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ymin = -Inf, ymax = Inf) +
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annotate("rect", fill = "#FFC87E", alpha = 0.4,
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xmin = 20.79, xmax = 25,
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ymin = -Inf, ymax = Inf) +
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geom_point(aes(shape = chemostat_ID, color = chemostat_ID), size = 2) +
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geom_line(aes(color = chemostat_ID, linetype = chemostat_ID)) +
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labs(y = expression (""), x = "Days After Start") +
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scale_color_manual(values = c("black", "black")) +
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pretty.theme()
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DOC_plot
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