Plot 77K fluorescence data
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1. Introduction
The analysis reported here is part of the manuscript Romand et al. 2021. The script plots 77K chlorophyll fluorescence data where averages and CI have already been calculated.
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") }
library(knitr)
library(ggplot2)
library(readxl)2. Data
Data is imported from an excel file containing a column for the wavelength x in nm, a column of fluorescence values y values, a column of 95% CI values ci, a column for the different lines line and a column for the different treatment conditions cond
data1 <- read_excel("77K.xlsx")3. Plot Graph
Graphs are now plotted.
# With 95% ci, all singing all dancing ZOOMED 660-710
p<-ggplot(data=data1, aes(x=x, y=y, fill=cond))+
geom_ribbon(aes(ymin=y-ci, ymax=y+ci,x=x, fill=cond),alpha=0.3)+
geom_line(data=data1,aes(x=x, y=y, color=cond), size=0.3)+
scale_fill_manual(values=c("black", "red"))+
scale_color_manual(values=c("black", "red"))+
scale_x_continuous(breaks=seq(660,710,20), limits=c(660,710))+
scale_y_continuous(breaks=seq(0,1,0.5), limits=c(-0.01,1.01))+
theme_classic()+
facet_grid(,vars(line))
print(p)
ggsave("zoom77K.pdf",width = 8, height = 3)
# With 95% ci, all singing all dancing FULL 650-800
p<-ggplot(data=data1, aes(x=x, y=y, fill=cond))+
geom_ribbon(aes(ymin=y-ci, ymax=y+ci,x=x, fill=cond),alpha=0.3)+
geom_line(data=data1,aes(x=x, y=y, color=cond), size=0.5)+
scale_fill_manual(values=c("black", "red"))+
scale_color_manual(values=c("black", "red"))+
scale_x_continuous(breaks=seq(650,800,100), limits=c(650,800))+
theme_classic()+
facet_grid(,vars(line))
print(p)
ggsave("full77K.pdf",width = 8, 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 Kingdom.1252
## ctype English_United Kingdom.1252
## tz Europe/Paris
## date 2021-07-15
##
## - 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 2.0-1 2021-05-04 [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 * 3.3.4 2021-06-16 [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)
## 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)
## memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0)
## munsell 0.5.0 2018-06-12 [1] 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)
## 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)
## 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)
## 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/Documents/R/win-library/4.1
## [2] C:/Program Files/R/R-4.1.0/library5. Citations
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.