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Mean_plot_trait_soils_regs.R
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##############################################################################
#
# L. Giraldo-Kalil Modificacion: 15 diciembre 2021
#
#
# Script para graficar media y error estandar de rasgos
# de cuatro especies de Damburneya respecto
# a suelos, por parcela. Los colores indican la especie,
# los simbolos de los puntos indican la altitud. Las lineas
# negras indican los valores promedio del rasgo por parcela
#
################################################################################
# Cargar librerias y datos
library(ggpubr)
library(ggplot2)
library(here)
library(xlsx)
library(purrr)
library(RColorBrewer)
library(purrr)
library(tidyverse)
library(plyr)
datos <- read.xlsx(here("Datos","Finales", "Mean_trait_values.xlsx"),1)
which(is.na(datos))
View(datos)
# reviso un poco de las columnas
#___________________________________________________________________________
#Cargar paleta colorblind-friendly :) -de Okabe e Ito
cbPalette <- c("#D55E00", "#0072B2",
"#E69F00", "#009E73",
"#F0E442", "#56B4E9",
"#CC79A7", "#999999")
#######################################################################
#_____________________________________________________________
#Reorganizo niveles para controlar output en el facet_wrap
# Convertir columnas categoricas en factores
tmp_factor <- c("species","Altitude","Trait","Plot")
datos[tmp_factor] <- lapply(datos[tmp_factor], factor)
#Reorganizo rasgos
neworder <- c("SLA","LDMC","LNmass","LPmass","LeafNP")
rasgos <- arrange(transform(datos,
Trait=factor(Trait,levels=neworder)),Trait)
View(rasgos)
levels(rasgos$Trait)
response_dat<-rasgos %>%
select(mean_trait_value_plot)
response <- names(response_dat)
response
expl_dat <- rasgos %>%
select(Clay,pH,SOC,STN,CNratio,NO3,NH4,STP,SAP)
expl <- names(expl_dat)
expl
########Funcion para graficar
scatter_fun = function(x, y)
{ggplot(rasgos, aes(x = .data[[x]],
y= weighted_mean_trait_plot
))+
geom_point(aes(shape=Altitude),
color= "black",
size=1)+
theme_classic()+
scale_fill_manual(values=cbPalette) +
scale_colour_manual(values=cbPalette)+
scale_shape_manual(values=c(15,16))+
geom_smooth(aes(y=weighted_mean_trait_plot),
show.legend = TRUE,
color= "black",
size=1, method=lm, se=F)+
geom_smooth(aes(y = sp_mean_trait_value,
color=species),
show.legend = TRUE,
linetype="dashed",
size=0.7, method=lm, se=F)+
# geom_point(aes(y = sp_mean_trait_value,
# color=species),
# size=1, shape=16)+
# geom_smooth(aes(y=mean_trait_values_plot,fill= "species"),
# size=0.5, method=lm,linetype="dashed",
# se=F)+
#geom_errorbar(aes(ymin=sp_mean_trait_value-Standard_error_mean,
# ymax=sp_mean_trait_value+Standard_error_mean),
# position=position_dodge(0.05))+
guides(fill = FALSE)+
theme(legend.position = c(1, 0),
legend.box.margin=margin(c(0,0,0,90)),
legend.box = "horizontal",
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
labs(colour = "Species")+
guides(fill = FALSE)+
theme(legend.position = "bottom",
legend.title=element_blank(),
legend.key.size = unit(0.8,"line"),
axis.text = element_text(size = 8),
axis.title= element_text(size= 9),
legend.text= element_text (size=8),
legend.box = "horizontal",
panel.border = element_rect(colour = "black", fill=NA),
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
ylab(NULL)+
facet_wrap(~Trait, scales = "free",
strip.position = "left",
ncol = 1,
labeller= as_labeller(c(SLA="SLA (cm^2/g)",
LDMC="LDMC(mg/g)",
LNmass="LNmass (mg/g)",
LPmass="LPmass (mg/g)",
LeafNP="Leaf~N:P"),
default = label_parsed))
}
#############################################
all_plots = map(response,
~map(expl, scatter_fun, y = .x)
)
#TODAS
a<-all_plots[[1]][[1]]+labs(x="Clay (%)")
b<-all_plots[[1]][[2]]
c<-all_plots[[1]][[3]]+labs(x="SOC (mg/g)")
d<-all_plots[[1]][[4]]+labs(x="STN (mg/g)")
e<-all_plots[[1]][[5]]+labs(x="C:N")
f<-all_plots[[1]][[6]]+labs(x=expression("NO"[3]*" ("*"µg/g)"))
g<-all_plots[[1]][[7]]+labs(x=expression("NH"[4]*" ("*"µg/g)"))
h<-all_plots[[1]][[8]]+labs(x=expression("STP ("*"µg/g)"))
i<-all_plots[[1]][[9]] +labs(x=expression("SAP ("*"µg/g)"))
#STN, NO3,NH4_todos los rasgos
Figure_4<-ggarrange(d,f,g,
ncol = 3, nrow = 1,
font.label = list(size = 10),
common.legend = TRUE, legend="bottom")
#_Figura Suplementaria:
#SOC_CN_STP___TODOS LOS RASGOS
Appendix_S7<-ggarrange(c,e,h,
ncol = 3, nrow = 1,
font.label = list(size = 10),
common.legend = TRUE, legend="bottom")
Figure_4
Appendix_S7
ggsave("Figure_4.pdf",
plot= Figure_4,
path = "Figuras",
device= "pdf",
height=9,
width=7.25,
units= "in", dpi=600)
ggsave("Appendix_S7.pdf",
plot= Appendix_S7,
path = "Figuras",
device= "pdf",
height=9,
width=7.25,
units= "in", dpi=600)
# Para figuras de SAP, clay, pH por tipos de rasgos
#nutrientes foliares
scatter_fun_nut = function(x, y)
{ggplot(subset(rasgos, Trait %in% c("LNmass", "LPmass", "LeafNP")),
aes(x = .data[[x]],
y= weighted_mean_trait_plot))+
geom_point(aes(shape=Altitude),
color= "black",
size=1)+
theme_classic()+
scale_fill_manual(values=cbPalette) +
scale_colour_manual(values=cbPalette)+
scale_shape_manual(values=c(15,16))+
geom_smooth(aes(y=weighted_mean_trait_plot),
show.legend = TRUE,
color= "black",
size=1, method=lm, se=F)+
geom_smooth(aes(y = sp_mean_trait_value,
color=species),
show.legend = TRUE,
linetype="dashed",
size=0.7, method=lm, se=F)+
guides(fill = FALSE)+
theme(legend.position = c(1, 0),
legend.box.margin=margin(c(0,0,0,90)),
legend.box = "horizontal",
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
labs(colour = "Species")+
guides(fill = FALSE)+
theme(legend.position = "bottom",
legend.title=element_blank(),
legend.key.size = unit(0.8,"line"),
axis.text = element_text(size = 8),
axis.title= element_text(size= 9),
legend.text= element_text (size=8),
legend.box = "horizontal",
panel.border = element_rect(colour = "black", fill=NA),
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
ylab(NULL)+
facet_wrap(~Trait, scales = "free",
strip.position = "left",
ncol = 1,
labeller= as_labeller(c(SLA="SLA (cm^2/g)",
LDMC="LDMC(mg/g)",
LNmass="LNmass (mg/g)",
LPmass="LPmass (mg/g)",
LeafNP="Leaf~N:P"),
default = label_parsed))
}
#############################################
all_plots_nut = map(response,
~map(expl, scatter_fun_nut, y = .x)
)
#Subplots:
j<-all_plots_nut[[1]][[1]]+labs(x="Clay (%)")
k<-all_plots_nut[[1]][[2]]
l<-all_plots_nut[[1]][[9]] +labs(x=expression("SAP ("*"µg/g)"))
###########
#SAP_pH_clay___Nutrientes foliares
Figure_3<-ggarrange(l,k,j,
ncol = 3, nrow = 1,
font.label = list(size = 10),
common.legend = TRUE, legend="bottom")
Figure_3
ggsave("Figure_3.pdf",
plot= Figure_3,
path = "Figuras",
device= "pdf",
height=6,
width=7.25,
units= "in", dpi=600)
###################
#morfol?gicos
scatter_fun_morf = function(x, y)
{ggplot(subset(rasgos, Trait %in% c("SLA", "LDMC")),
aes(x = .data[[x]],
y = weighted_mean_trait_plot))+
geom_point(aes(shape=Altitude),
color= "black",
size=1)+
theme_classic()+
scale_fill_manual(values=cbPalette) +
scale_colour_manual(values=cbPalette)+
scale_shape_manual(values=c(15,16))+
geom_smooth(aes(y=weighted_mean_trait_plot),
show.legend = TRUE,
color= "black",
size=1, method=lm, se=F)+
geom_smooth(aes(y = sp_mean_trait_value,
color=species),
show.legend = TRUE,
linetype="dashed",
size=0.7, method=lm, se=F)+
guides(fill = FALSE)+
theme(legend.position = c(1, 0),
legend.box.margin=margin(c(0,0,0,90)),
legend.box = "horizontal",
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
labs(colour = "Species")+
guides(fill = FALSE)+
theme(legend.position = "bottom",
legend.title=element_blank(),
legend.key.size = unit(0.8,"line"),
axis.text = element_text(size = 8),
axis.title= element_text(size= 9),
legend.text= element_text (size=8),
legend.box = "horizontal",
panel.border = element_rect(colour = "black", fill=NA),
strip.text.x = element_text(hjust = 1, face="bold",
margin=margin(0,0,0,0)),
strip.background = element_rect(colour=NA),
strip.placement = "outside")+
ylab(NULL)+
facet_wrap(~Trait, scales = "free",
strip.position = "left",
ncol = 1,
labeller= as_labeller(c(SLA="SLA (cm^2/g)",
LDMC="LDMC(mg/g)",
LNmass="LNmass (mg/g)",
LPmass="LPmass (mg/g)",
LeafNP="Leaf~N:P"),
default = label_parsed))
}
#############################################
all_plots_morf = map(response,
~map(expl, scatter_fun_morf, y = .x)
)
#Subplots:
m<-all_plots_morf[[1]][[1]]+labs(x="Clay (%)")
n<-all_plots_morf[[1]][[2]]
o<-all_plots_morf[[1]][[9]] +labs(x=expression("SAP ("*"µg/g)"))
#Figura suplementaria
#SAP_pH_clay___Nutrientes foliares
Appendix_S8<-ggarrange(o,n,m,
ncol = 3, nrow = 1,
font.label = list(size = 10),
common.legend = TRUE, legend="bottom")
Appendix_S8
ggsave("Appendix_S8.pdf",
plot= Appendix_S8,
path = "Figuras",
device= "pdf",
height=4,
width=7.25,
units= "in", dpi=600)