# Plot ETR

#### ----

## 1. Introduction

The analysis reported here is part of the manuscript Romand et al. 2021. The script plots ETR data.

### Setup R packages

    if (!require(knitr)) { install.packages("knitr", repos = "http://cran.us.r-project.org") }
    if (!require(ggplot2)) { install.packages("ggplot2", repos = "http://cran.us.r-project.org") }
    if (!require(dplyr)) { install.packages("dplyr", repos = "http://cran.us.r-project.org") }
    if (!require(readxl)) { install.packages("readxl", repos = "http://cran.us.r-project.org") }
    if (!require(Rmisc)) { install.packages("Rmisc", repos = "http://cran.us.r-project.org") }
    if (!require(svglite)) { install.packages("svglite", repos = "http://cran.us.r-project.org") }

    library(knitr)
    library(ggplot2)
    library(dplyr)
    library(readxl)
    library(Rmisc)
    library(svglite)

## 2. Data

Data is imported from an excel file containing a column of line names `line`, a column of ETR values `etr`, and a column of light intensity values `light`. A facet plot can be used to plot a graph for different treatments.

    # Import data

    data <- read_excel("etr.xlsx", col_types = c("numeric", "text", "text", "numeric", "numeric"))

## 3. Plot Graph

A graph is now plotted with all lines together.

    # Take a subset of lines and do summary stats

    sumdata=summarySE(data, measurevar="etr", groupvars=c("line","light"))

    # Plot graph

    p<-ggplot(data=data, aes(x=light, y=etr, fill=line))+
      geom_ribbon(data=sumdata,aes(ymin=etr-ci, ymax=etr+ci,x=light, color=line),alpha=0.3, fill="purple",linetype=0)+
      geom_smooth(data=data, aes(x=light, y=etr, fill=line), alpha=0.6, se=FALSE, color="purple")+
      geom_point(data=sumdata, aes(x=light,y=etr, fill=line), alpha=0.4, color="magenta", size=2)+
      scale_x_continuous(limits=c(0,500),expand = c(0, 0))+
      theme_classic()+
      theme(legend.position="bottom")
    p

    ggsave("ETRN50.pdf", width=1.5, height=3)
    ggsave("ETRN50.svg", width=1.5, height=3)

## 4. R session information

    InfoSession <- devtools::session_info()
    print(InfoSession)

    ## - Session info ---------------------------------------------------------------
    ##  setting  value
    ##  version  R version 4.1.0 (2021-05-18)
    ##  os       Windows 10 x64
    ##  system   x86_64, mingw32
    ##  ui       RTerm
    ##  language (EN)
    ##  collate  English_United States.1252
    ##  ctype    English_United States.1252
    ##  tz       Europe/Paris
    ##  date     2021-06-29
    ##
    ## - Packages -------------------------------------------------------------------
    ##  package     * version date       lib source
    ##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
    ##  cachem        1.0.5   2021-05-15 [1] CRAN (R 4.1.0)
    ##  callr         3.7.0   2021-04-20 [1] CRAN (R 4.1.0)
    ##  cellranger    1.1.0   2016-07-27 [1] CRAN (R 4.1.0)
    ##  cli           2.5.0   2021-04-26 [1] CRAN (R 4.1.0)
    ##  colorspace    2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
    ##  crayon        1.4.1   2021-02-08 [1] CRAN (R 4.1.0)
    ##  DBI           1.1.1   2021-01-15 [1] CRAN (R 4.1.0)
    ##  desc          1.3.0   2021-03-05 [1] CRAN (R 4.1.0)
    ##  devtools      2.4.2   2021-06-07 [1] CRAN (R 4.1.0)
    ##  digest        0.6.27  2020-10-24 [1] CRAN (R 4.1.0)
    ##  dplyr       * 1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
    ##  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
    ##  evaluate      0.14    2019-05-28 [1] CRAN (R 4.1.0)
    ##  fansi         0.5.0   2021-05-25 [1] CRAN (R 4.1.0)
    ##  farver        2.1.0   2021-02-28 [1] CRAN (R 4.1.0)
    ##  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
    ##  fs            1.5.0   2020-07-31 [1] CRAN (R 4.1.0)
    ##  generics      0.1.0   2020-10-31 [1] CRAN (R 4.1.0)
    ##  ggplot2     * 3.3.5   2021-06-25 [1] CRAN (R 4.1.0)
    ##  glue          1.4.2   2020-08-27 [1] CRAN (R 4.1.0)
    ##  gtable        0.3.0   2019-03-25 [1] CRAN (R 4.1.0)
    ##  highr         0.9     2021-04-16 [1] CRAN (R 4.1.0)
    ##  htmltools     0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
    ##  knitr       * 1.33    2021-04-24 [1] CRAN (R 4.1.0)
    ##  labeling      0.4.2   2020-10-20 [1] CRAN (R 4.1.0)
    ##  lattice     * 0.20-44 2021-05-02 [2] CRAN (R 4.1.0)
    ##  lifecycle     1.0.0   2021-02-15 [1] CRAN (R 4.1.0)
    ##  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.1.0)
    ##  Matrix        1.3-3   2021-05-04 [2] CRAN (R 4.1.0)
    ##  memoise       2.0.0   2021-01-26 [1] CRAN (R 4.1.0)
    ##  mgcv          1.8-35  2021-04-18 [2] CRAN (R 4.1.0)
    ##  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
    ##  nlme          3.1-152 2021-02-04 [2] CRAN (R 4.1.0)
    ##  pillar        1.6.1   2021-05-16 [1] CRAN (R 4.1.0)
    ##  pkgbuild      1.2.0   2020-12-15 [1] CRAN (R 4.1.0)
    ##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
    ##  pkgload       1.2.1   2021-04-06 [1] CRAN (R 4.1.0)
    ##  plyr        * 1.8.6   2020-03-03 [1] CRAN (R 4.1.0)
    ##  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.1.0)
    ##  processx      3.5.2   2021-04-30 [1] CRAN (R 4.1.0)
    ##  ps            1.6.0   2021-02-28 [1] CRAN (R 4.1.0)
    ##  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
    ##  R6            2.5.0   2020-10-28 [1] CRAN (R 4.1.0)
    ##  Rcpp          1.0.6   2021-01-15 [1] CRAN (R 4.1.0)
    ##  readxl      * 1.3.1   2019-03-13 [1] CRAN (R 4.1.0)
    ##  remotes       2.4.0   2021-06-02 [1] CRAN (R 4.1.0)
    ##  rlang         0.4.11  2021-04-30 [1] CRAN (R 4.1.0)
    ##  rmarkdown     2.9     2021-06-15 [1] CRAN (R 4.1.0)
    ##  Rmisc       * 1.5     2013-10-22 [1] CRAN (R 4.1.0)
    ##  rprojroot     2.0.2   2020-11-15 [1] CRAN (R 4.1.0)
    ##  scales        1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
    ##  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.1.0)
    ##  stringi       1.6.1   2021-05-10 [1] CRAN (R 4.1.0)
    ##  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
    ##  svglite     * 2.0.0   2021-02-20 [1] CRAN (R 4.1.0)
    ##  systemfonts   1.0.2   2021-05-11 [1] CRAN (R 4.1.0)
    ##  testthat      3.0.3   2021-06-16 [1] CRAN (R 4.1.0)
    ##  tibble        3.1.2   2021-05-16 [1] CRAN (R 4.1.0)
    ##  tidyselect    1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
    ##  usethis       2.0.1   2021-02-10 [1] CRAN (R 4.1.0)
    ##  utf8          1.2.1   2021-03-12 [1] CRAN (R 4.1.0)
    ##  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
    ##  withr         2.4.2   2021-04-18 [1] CRAN (R 4.1.0)
    ##  xfun          0.24    2021-06-15 [1] CRAN (R 4.1.0)
    ##  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.1.0)
    ##
    ## [1] C:/Users/Ben Field/Documents/R/win-library/4.1
    ## [2] C:/Program Files/R/R-4.1.0/library

## 5. Citations

1. R Core Team. 2020. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

2. Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.

3. Wickham, Hadley, and Jennifer Bryan. 2019. Readxl: Read Excel Files. https://CRAN.R-project.org/package=readxl.

4. Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2021. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.

5. Hope, Ryan M. 2013. Rmisc: Rmisc: Ryan Miscellaneous. https://CRAN.R-project.org/package=Rmisc.