other_controls.Rmd

---
title: "Analysis: Other Controls"
author: "Silverman et al."
date: "`r format(Sys.Date(), '%d %b %Y')`"
output:
  html_document: 
    css: stylesheet.css
    fig_caption: yes
    number_sections: yes
    toc: yes
    toc_float: true
    toc_depth: 3
    code_folding: show
subtitle: "Source file: [SI GitHub Repository](http://www.github.com/KopfLab/2018_Silverman_et_al/) / [isotope_calibration.Rmd](http://www.github.com/KopfLab/2018_Silverman_et_al/blob/master/other_controls.Rmd)"
editor_options:
  chunk_output_type: inline
---


```{r setup, echo = FALSE, message=FALSE, warning=FALSE}
library(tidyverse) # dplyr, tidyr, ggplot
library(latex2exp) # for latex plot labels
library(readxl) # read excel file
source(file.path("lib", "functions.R"))
knitr::opts_chunk$set(
  dev=c("png", "pdf"), dev.args=list(pdf = list(encoding="WinAnsi", useDingbats=FALSE)),
  fig.keep="all", fig.path=file.path("figures", "2018_Silverman_et_al-"))
```

# Growth without nitrogen fixation (BG11+ medium)

*Anabaena cylindrica* growing in nitrate replete medium (BG11+) under different partial pressure of N2.

```{r "SI_BG11+_control", fig.width = 6, fig.height = 4}
# read data
read_excel(
  file.path("data", "2018_Silverman_et_al-controls_data.xlsx"), 
  sheet = "BG11+") %>% 
  # plot
  ggplot() +
  # plot-wide aesthetics
  aes(x = day, y = OD750, shape = type, 
      color = paste(pN2, "bar"), fill = paste(pN2, "bar")) +
  # all data (small translucent points)
  geom_point(size = 2, alpha = 0.5, color = "black") +
  # averages and lines connection them
  stat_summary(fun.y = mean, geom = "line", size = 1) +
  stat_summary(fun.y = mean, geom = "point", color = "black", size = 4) +
  # scale
  scale_x_continuous(breaks = 0:10) +
  scale_color_manual(values = cbPalette[c(2,5)]) +
  scale_fill_manual(values = cbPalette[c(2,5)]) +
  scale_shape_manual(values = c(21:26)) +
  # labels
  labs(x = "day", y = TeX("$OD_{750}$"), shape = "", 
       color = expression("pN"[2]), fill = expression("pN"[2])) +
  # theme
  theme_figure() +
  guides(fill = guide_legend(override.aes = list(shape = 21)))
```