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  • usadellab/quinoa_chileanfieldtrial
  • ceplas/quinoa_chileanfieldtrial_c
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studies/ExperimentalSetup/trialplots_quinoa.png

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studies/Quinoaimage3.jpeg

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studies/Quinoaimage6.jpeg

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studies/Quinoaimage8.jpeg

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This ARC consists of one study- a field trial conducted at the INIA-Huasco experimental center located in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) during the 2019/2020 growing season (sowing on 26 September 2019, harvest on 21 February 2020).
Please view the [Experimental Setup](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/studies/ExperimentalSetup?ref_type=heads) for a full description.
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<img src="Quinoaimage8.jpeg" width="40%" />
<img src="Quinoaimage3.jpeg" width="50%" />
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#Load libraries
library(dplyr)
library(ggplot2)
library(tidyverse)
library(lubridate)
library(ggpubr)
#set working directory
setwd("~/Documents/QuinoaDiveristy/FIELDTRIAL_publicationdata/FieldTrial_R/WeatherData")
#import Night data
Envdata_Night<- read.csv(file = "EnvironmentAll_night_values.csv", head = TRUE, sep = ' ')
#Calculate mean temp per night
EnvdataNight_meantemp <- Envdata_Night %>% dplyr::group_by(das) %>% summarise(mean(AT_DEGC, na.rm = TRUE))
#import Day data
Envdata_Day<- read.csv(file = "EnvironmentAll_Day_values.csv", head = TRUE, sep = ' ')
#Calculate parameters
#Daily Max temp
EnvdataDay_maxtemp <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(max(AT_DEGC, na.rm = TRUE))
#Daily max VDP
EnvdataDay_maxVPD <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(max(VPD_kPa, na.rm = TRUE))
#Daily sum Radiation
EnvdataDay_sumRAD <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(sum(RAD_maxWM2, na.rm = TRUE))
#Rename columns
#Daily max temp
colnames(EnvdataDay_maxtemp)
names (EnvdataDay_maxtemp)[names(EnvdataDay_maxtemp) == "max(AT_DEGC, na.rm = TRUE)"] <- "Daily_MaxTemp"
#Average night temp
colnames(EnvdataNight_meantemp)
names (EnvdataNight_meantemp)[names(EnvdataNight_meantemp) == "mean(AT_DEGC, na.rm = TRUE)"] <- "Nightly_MeanTemp"
#Daily max VPD
colnames(EnvdataDay_maxVPD)
names (EnvdataDay_maxVPD)[names(EnvdataDay_maxVPD) == "max(VPD_kPa, na.rm = TRUE)"] <- "Daily_MaxVPD"
#Daily sum RAD
colnames(EnvdataDay_sumRAD)
names (EnvdataDay_sumRAD)[names(EnvdataDay_sumRAD) == "sum(RAD_maxWM2, na.rm = TRUE)"] <- "Daily_sumRAD"
#Day and Night Temperatures
Temps_all <- cbind(EnvdataDay_maxtemp$das, EnvdataDay_maxtemp$Daily_MaxTemp,
EnvdataNight_meantemp$Nightly_MeanTemp)
tempheadings <- c("das", "Daily_MaxTemp", "Nightly_MeanTemp")
colnames(Temps_all) <- tempheadings
Temps_DayNight <- as.data.frame(Temps_all)
#Import SWC data
SWCData<- read.csv(file = "~/Documents/QuinoaDiveristy/FIELDTRIAL_publicationdata/FieldTrial_R/WeatherData/SoilVWC_averages.csv", head = TRUE, sep = ' ')
SWCData_WWmeanSWC <- SWCData %>% dplyr::group_by(das) %>% summarise(mean(soilVWC_WW))
SWCData_WDmeanSWC <- SWCData %>% dplyr::group_by(das) %>% summarise(mean(soilVWC_WD))
#Soil Water Content data
SWCData_meanVWC<- cbind(SWCData_WWmeanSWC$das, SWCData_WWmeanSWC$`mean(soilVWC_WW)`, SWCData_WDmeanSWC$`mean(soilVWC_WD)`)
headings <-c("das", "SWC_WW", "SWC_WD")
colnames(SWCData_meanVWC) <- headings
SWCData_VWC <- as.data.frame(SWCData_meanVWC)
class(SWCData_VWC[,3])
levels(SWCData_VWC)
#reorder levels
#line graphs
#MaxTempLG <-EnvdataDay_maxtemp %>%
#ggplot(aes (x=das, y=Daily_MaxTemp)) +
# geom_line()+
#theme(panel.grid = element_blank())+
#labs(y= expression( Temperature~(degree*C)),
# title= "Daily Maximum Temperature")
#MeanTempNightLG <-EnvdataNight_meantemp %>%
# ggplot(aes (x=das, y=Nightly_MeanTemp)) +
# geom_line()+
# theme(panel.grid = element_blank())+
# labs(y= expression( Temperature~(degree*C)),
# title= "Nightly Average Temperature")
temperatures <- rep(c("solid", "dashed"),2)
AllTempsLG <- Temps_DayNight %>%
ggplot(aes (x=das)) +
annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf,
fill="palegreen2", alpha=0.5)+
annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf,
fill="paleturquoise2", alpha=0.7)+
annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf,
fill="gray80", alpha=0.5)+
geom_line(aes(y=Daily_MaxTemp, linetype="Daily Maximum Temperature"))+
geom_line(aes(y=Nightly_MeanTemp, linetype="Nightly Mean Temperature"))+
labs(y= expression(Temperature~(degree*C)),
title= "Daily Maximum and Nightly Average Temperatures",
x= "Days after sowing")+
theme(panel.grid = element_blank(),
panel.background = element_rect(fill= "White"),
panel.border = element_blank(),
axis.line = element_line(),
legend.title = element_blank(),
legend.position = c(0.5,1.10),
legend.direction ="horizontal",
legend.background= element_rect(fill=NA),
legend.key=element_blank()) +
scale_linetype_manual(values = temperatures) +
scale_x_continuous(expand = c(0,0))+
scale_fill_discrete(name=NULL)
AllTempsLG
MaxVPDLG <-EnvdataDay_maxVPD %>%
ggplot(aes (x=das, y=Daily_MaxVPD)) +
annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf,
fill="palegreen2", alpha=0.5)+
annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf,
fill="paleturquoise2", alpha=0.7)+
annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf,
fill="gray80", alpha=0.5)+
theme(panel.grid = element_blank())+
geom_line()+
labs(y= expression( VPD~(kPa) ),
title= "Daily Maximum Vapor-Pressure Deficit", x= "Days after sowing")+
theme(panel.grid = element_blank(),
panel.background = element_rect(fill= "White"),
panel.border = element_blank(),
axis.line = element_line(),
legend.title = element_blank()) +
scale_x_continuous(expand = c(0,0))+
scale_fill_discrete(name=NULL)
MaxVPDLG
SumRADLG <-EnvdataDay_sumRAD %>%
ggplot(aes (x=das, y=Daily_sumRAD)) +
annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf,
fill="palegreen2", alpha=0.5)+
annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf,
fill="paleturquoise2", alpha=0.7)+
annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf,
fill="gray80", alpha=0.5)+
geom_line()+
theme(panel.grid = element_blank())+
labs(y= expression(Radiation~(W/m^2)),
title= "Daily Total Radiation", x= "Days after sowing")+
theme(panel.grid = element_blank(),
panel.background = element_rect(fill= "White"),
panel.border = element_blank(),
axis.line = element_line(),
legend.title = element_blank()) +
scale_x_continuous(expand = c(0,0))+
scale_fill_discrete(name=NULL)
treatment <- c("solid", "dashed")
SumSWCLG <-SWCData_VWC %>%
ggplot(aes (x=das)) +
annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf,
fill="palegreen2", alpha=0.5)+
annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf,
fill="paleturquoise2", alpha=0.7)+
annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf,
fill="gray80", alpha=0.5)+
geom_line(aes(y=SWC_WW, linetype="Full Irrigation"))+
geom_line(aes(y=SWC_WD, linetype="Reduced Irrigation"))+
labs(y= expression(VSWC~(m^3*m^3)),
title= "Daily Volumetric Soil Water Content", x= "Days after sowing")+
theme(panel.grid = element_blank(),
panel.background = element_rect(fill= "White"),
panel.border = element_blank(),
axis.line = element_line(),
legend.title = element_blank(),
legend.position = c(0.5,1.10),
legend.direction ="horizontal",
legend.background= element_rect(fill=NA),
legend.key=element_blank())+
scale_linetype_manual(values = treatment, breaks=c("Full Irrigation","Reduced Irrigation"))+
scale_x_continuous(expand = c(0,0))
SumSWCLG
background <- SWCData_WDmeanSWC %>%
ggplot(aes (x=das, y="mean(soilVWC_WD)")) +
annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf,
fill="palegreen2", alpha=0.5)+
annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf,
fill="paleturquoise2", alpha=0.7)+
annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf,
fill="gray80", alpha=0.5)+
theme(panel.grid = element_blank(),
panel.background = element_rect(fill= "White"),
panel.border = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank())+
scale_x_continuous(expand = c(0,0))+
labs(y=" ", x=" ")+
geom_line()
background
figure <- ggarrange(AllTempsLG, MaxVPDLG, SumRADLG, SumSWCLG, background,
labels = c("A", "B", "C", "D", " "),
ncol = 1, nrow = 5, align = "v")
figure
colnames(SWCData_WDmeanSWC)
#Graphs with different rectangle colors
MaxTempLG <-EnvdataDay_maxtemp %>%
ggplot(aes (x=das, y=Daily_MaxTemp)) +
geom_line()+
theme(panel.grid = element_blank())+
labs(y= expression( Temperature~(degree*C)),
title= "Daily Maximum Temperature")+
geom_rect(aes(xmin=0, xmax=60, ymin=-Inf, ymax=Inf),
fill= 'gray100', alpha = 0.002)+
geom_rect(aes(xmin=60, xmax=105, ymin=-Inf, ymax=Inf),
fill= 'gray78', alpha = 0.002)+
geom_rect(aes(xmin=105, xmax=156, ymin=-Inf, ymax=Inf),
fill= 'gray61', alpha = 0.002)