Appendix 13
C. Prévost & A. Suryanarayan
2023-07-14
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = 'C:\\Users\\camie\\Dropbox\\Dropbox\\Beg ar Loued\\Article AS_CP\\BAL R data and scripts\\clean_R_scripts\\data_for_figures')##This R Markdown document provides the code for all figures in Prevost and Suryanarayan et al. to ensure transparency and reproducibility of data.
INSTRUCTIONS
#1) Please ensure you have downloaded the latest version of R Studio.
#2) Download data files from the data repository.
#3) Change file pathway to the name of the folder where you have saved the data files.
##publication order:
#FIG. 5
#FIG. 6
–
FIG. 5
#Load packages
library(readr)
library(readxl)
library(ggplot2)
library(patchwork)
library(ggrepel)#Load data and verification
Pathway <- 'C:/Users/camie/Dropbox/Dropbox/Beg ar Loued/Article AS_CP/BAL R data and scripts/clean_R_scripts/data_for_figures'
setwd(Pathway)
tt <- read_excel ("data_fig4_iso_v2.xls", sheet = "archeo")
ref <- read_excel("data_fig4_iso_refs.xls", sheet = "ref")
dim (tt)## [1] 24 12head(ref)head(tt)#Convert variables to factors
tt$nomech <- as.factor(tt$nomech)
tt$gr <- as.factor(tt$gr)
tt$new_chrono <- as.factor(tt$US2)#Define x, y and z
x=tt$d13C16MEcorr
y=tt$d13C18MEcorr
z=expression(list(Delta ^"13" ~"C"))
zz=expression("Sample identification clusters")
zzz=expression("Published references")
g=-3.3#Preparing Figure 5
n3<-ggplot(tt, aes(x, y)) +
stat_density_2d(data=ref,
aes(x=d13C16MEcorr,y=d13C18MEcorr,
alpha = (..level..) ^ 2, fill = cat),
geom = "polygon", contour_var = "ndensity", bins=7)+
scale_alpha_continuous(name=zz,range = c(0, 0.7))+
guides(fill = guide_legend(title = zzz))+
scale_fill_manual(values=c('turquoise2','#8cb9b2', 'royalblue','red','lightgreen','#ff89dc'))+
labs(x=expression(list(delta^"13" ~"C"[16:0~MEcorr])),
y=expression(list(delta^"13" ~"C"[18:0~MEcorr])),
size=1.5)+
scale_y_continuous(limits=c(-40,-20))+
theme_minimal() +
facet_wrap(facets = vars(US2), strip.position = c("top"))+
theme(legend.title = element_text(size = 10),
strip.text = element_text(size=12, color = 'black'),
strip.placement = "outside",
strip.background = element_rect(fill = "#eaecee", colour = "black", size = 0.5)
)## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.#Preparing Figure 5: add reference data points
n4<-n3+ geom_point(aes(color=Delta13CcorrME, shape=gr), alpha=1, size=2.5)+
scale_shape_manual(name=zz,values=c(15,17,19,18), labels=c("Milk","Ruminant", "Unspecific"))+
geom_vline(xintercept = -30, linetype = "dotted",colour = "black") +
geom_vline(xintercept = -27, linetype = "dashed",colour = "grey", size=0.15) +
geom_vline(xintercept = -24, linetype = "dotted",colour = "black") +
scale_colour_gradient2(name=z,low = "#fc49ff",mid = "#05b400",high = "#111218",midpoint =-1.5)+
geom_rug(aes(color=Delta13CcorrME))+
scale_x_continuous(expand = expansion(0))## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.#Preparing Figure 5: add colours and annotations
n5<- n4+
annotate(geom ="rect", xmin = -40, xmax = -27, ymin = -40, ymax = -39,alpha = 0.1, fill = "green")
n6<- n5+
annotate(geom ="rect", xmin = -27, xmax = -20, ymin = -40, ymax = -39, alpha = .1, fill = "dodger blue")
n7<- n6+
annotate("text", x = c(-23), y = (-39.5),label = c(">>Incr. Marine diet"),colour = c("royalblue"), size=3)
n8<- n7+
annotate("text", x = c(-33), y = (-39.5),label = c("Incr.C3 diet <<"),colour = c("palegreen4"), size=3)
n9<- n8+
annotate(geom ="rect", xmin = -24, xmax = -20, ymin = -39, ymax = -38,alpha = 0.2, fill = "blue")
n10<- n9+
annotate(geom ="rect", xmin = -40, xmax = -27, ymin = -39, ymax = -38, alpha = .2, fill = "turquoise2")
n11<- n10+
annotate(geom ="rect", xmin = -30, xmax = -26, ymin = -39, ymax = -38, alpha = .2, fill = "rosybrown4")
n12<- n11+
annotate("text", x = c(-34), y = (-38.5),label = c("Freshwater"),colour = c("turquoise4"),size=3)
n13<- n12+
annotate("text", x = c(-22), y = (-38.5),label = c("Marine"),colour = c("royalblue3"),size=3)
n14<- n13+
annotate("text", x = c(-27), y = (-38.5),label = c("Terrestrial"),colour = c("rosybrown4"),size=3)
n14## Warning: The dot-dot notation (`..level..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(level)` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: Removed 9 rows containing non-finite values (`stat_density2d()`).
FIG. 6
#Load packages
library(dplyr) ##
## Attachement du package : 'dplyr'## Les objets suivants sont masqués depuis 'package:stats':
##
## filter, lag## Les objets suivants sont masqués depuis 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(plyr)## ------------------------------------------------------------------------------## You have loaded plyr after dplyr - this is likely to cause problems.
## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
## library(plyr); library(dplyr)## ------------------------------------------------------------------------------##
## Attachement du package : 'plyr'## Les objets suivants sont masqués depuis 'package:dplyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarizelibrary(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ lubridate 1.9.2 ✔ tibble 3.2.1
## ✔ purrr 1.0.1 ✔ tidyr 1.3.0## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ plyr::arrange() masks dplyr::arrange()
## ✖ purrr::compact() masks plyr::compact()
## ✖ plyr::count() masks dplyr::count()
## ✖ plyr::desc() masks dplyr::desc()
## ✖ plyr::failwith() masks dplyr::failwith()
## ✖ dplyr::filter() masks stats::filter()
## ✖ plyr::id() masks dplyr::id()
## ✖ dplyr::lag() masks stats::lag()
## ✖ plyr::mutate() masks dplyr::mutate()
## ✖ plyr::rename() masks dplyr::rename()
## ✖ plyr::summarise() masks dplyr::summarise()
## ✖ plyr::summarize() masks dplyr::summarize()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(ggthemes)#Load data and verification
Pathway <- "C:/Users/camie/Dropbox/Dropbox/Beg ar Loued/Article AS_CP/BAL R data and scripts/clean_R_scripts/data_for_figures"
setwd(Pathway)
df <- read_excel("data_fig_supp_2.xls", sheet = "slip")
df$type <- factor(df$type)
df_sorted <- arrange(df, id)
str(df)## tibble [14 × 6] (S3: tbl_df/tbl/data.frame)
## $ id : chr [1:14] "MR6507" "MR6507" "MR6507" "MR6510" ...
## $ nom_ech: chr [1:14] "1 (SE)" "2 (T)" "3 (SI)" "1 (SE)" ...
## $ qt : num [1:14] 4368 452 678 303 109 ...
## $ type : Factor w/ 2 levels "coating","surface": 1 1 1 2 2 1 1 1 1 1 ...
## $ qtprc : num [1:14] 100 10.3 15.5 100 36.1 ...
## $ type2 : chr [1:14] "SE" "T" "SI" "SE" ...plot(df)
#Plotting Figure 6: Geom_bar chart
n5<-ggplot(df_sorted, aes (x=nom_ech, y=qtprc, fill=type2))+
scale_fill_manual(values=c("#9d91a6", "#4d3560", "#6a5c76"))+
geom_bar(stat= "identity", show.legend = FALSE, width = 0.80)+
scale_y_continuous(limits=c(0,100))+
facet_wrap(~id, ncol=6, scales = "free") +
labs(title = "TLE of samples from sherds with surface/coating layers", y = "Percentage")+
xlab("")+
theme_minimal()
leg<-element_text(color = "black", size = 6, angle=90, vjust = 0.4)
n6<-n5+theme(axis.text.x =leg, legend.background = element_rect(colour = NA))
n7<-n6+theme(panel.grid.minor = element_line(colour="white"))
n7