The analysis reported here is part of the manuscript Romand et al. 2021. The script plots ETR data.
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)
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.
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
## - 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
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##
## [1] C:/Users/Ben Field/Documents/R/win-library/4.1
## [2] C:/Program Files/R/R-4.1.0/library
R Core Team. 2020. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
Wickham, Hadley, and Jennifer Bryan. 2019. Readxl: Read Excel Files. https://CRAN.R-project.org/package=readxl.
Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2021. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
Hope, Ryan M. 2013. Rmisc: Rmisc: Ryan Miscellaneous. https://CRAN.R-project.org/package=Rmisc.