Acidity_plot_testa_grano_final.R

setwd("~/Library/CloudStorage/GoogleDrive-icarounam@gmail.com/Mi unidad/Agrosavia/Colaboraciones/René/1er_Cd/data")
datos<-read.table("todos_phys.csv", header=T, sep=',')
datos$curva <- factor(datos$curva, levels = c("1", "2","3"), 
                      labels = c("T3", "T1","T2"))
datos$gen<-as.factor(datos$gen)
datos$curva<-as.factor(datos$curva)
datos$id<-as.factor(datos$id)
datos$muestra<-as.factor(datos$muestra)
datos$dia<-as.factor(datos$dia)
library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.1.2

library(Rmisc)

## Loading required package: lattice

## Loading required package: plyr

library(dplyr)

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##     summarize

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library(tidyverse)

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library(ggpubr)

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library(rstatix)

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## Gráficas por réplica y genotipo
datos$dia<-as.numeric(as.character(datos$dia))
##Gráfica por réplica compuesta
pht<- ggplot(datos, aes(x = dia)) +
  facet_grid(curva~gen*muestra) +
  geom_line(aes(y=acidez.testa, linetype = "acidez.testa")) +
  geom_point(aes(y=acidez.testa, colour = "acidez.testa")) +
  scale_y_continuous(name = expression("Acidity")) +  # Etiqueta de la variable continua
  scale_x_continuous(name = "day", breaks=seq(0,7,1)) + # Etiqueta de los grupos
  theme(legend.position="bottom") +
  theme(axis.line = element_line(colour = "black", # Personalización del tema
                                 linewidth = 0.25)) +
  theme(text = element_text(size = 12))

pht3<-pht+ geom_line(aes(y = acidez.grano, linetype="acidez.grano")) + geom_point(aes(y=acidez.grano, colour = "acidez.grano")) + 
  theme(legend.position="bottom")
pht3 + scale_colour_discrete(name ="", labels=c('Nib', 'Testa')) + scale_linetype_discrete(name="",labels=c('Nib', 'Testa')) +
  geom_rug()

## Gráfica por genotipo

datos4<-summarySE (datos, measurevar = "acidez.testa", groupvars = c("curva", "gen","dia"))
datos5<-summarySE (datos, measurevar = "acidez.grano", groupvars = c("curva", "gen","dia"))
datos4$ID <- seq.int(nrow(datos4))
datos5$ID <- seq.int(nrow(datos5))
total2 <- merge (datos4, datos5, by = "ID")

### Guardando bases

write.csv(datos4, "~/Library/CloudStorage/GoogleDrive-icarounam@gmail.com/Mi unidad/Agrosavia/Colaboraciones/René/1er_Cd/data_out/Acidity_muestra_testa.csv")
write.csv(datos5, "~/Library/CloudStorage/GoogleDrive-icarounam@gmail.com/Mi unidad/Agrosavia/Colaboraciones/René/1er_Cd/data_out/Acidity_muestra_grano.csv")

pht2<- ggplot(total2, aes(x = dia.x)) +
  facet_grid(curva.x~gen.x) +
  geom_errorbar(aes(ymin=acidez.testa-ci.x, ymax=acidez.testa+ci.x, colour="acidez.testa"), width=.1) +
  geom_line(aes(y=acidez.testa, linetype="acidez.testa")) +
  geom_point(aes(y=acidez.testa, colour="acidez.testa")) +
  scale_y_continuous(name = expression("Acidity")) +  # Etiqueta de la variable continua
  scale_x_continuous(name = "day", breaks=seq(0,7,1)) + # Etiqueta de los grupos
  theme(legend.position="bottom") +
  theme(axis.line = element_line(colour = "black", # Personalización del tema
                                 linewidth = 0.25)) +
  theme(text = element_text(size = 15))

pht4<-pht2+ geom_errorbar(aes(ymin=acidez.grano-ci.y, ymax=acidez.grano+ci.y, colour="acidez.grano"), width=.1) +
  geom_line(aes(y=acidez.grano, linetype="acidez.grano")) +
  geom_point(aes(y=acidez.grano, colour = "acidez.grano"))

pht4 + scale_colour_discrete(name ="", labels=c('Nib', 'Testa')) + scale_linetype_discrete(name="",labels=c('Nib', 'Testa')) +
  theme_bw() + theme_light() + geom_rug()