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Ferreira_Santos_et_al_scripts_BIVARIATE.R
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Ferreira_Santos_et_al_scripts_BIVARIATE.R
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#############################################################################
#############################################################################
# 0.0 IMPORTS
require(vegan)
require(ncf)
require(SoDA)
require(ggplot2)
require(cowplot)
require(ggpubr)
#############################################################################
#############################################################################
# 0.2 DATA COLLECTION
setwd(choose.dir())
getwd()
# Correlogram spline bivariate with function "spline.correlog"
ab<-read.table("abundance.txt", h=T)
xy<-read.table("xy.txt", h=T)
# data transformation by total
ab.rel<-decostand(ab, "total")
# Correlogram spline bivariate with ggplot2
Fin_Poc_gg<- read.table("1_Fin_poc_ggplot.txt", h=T)
Fin_Fol_gg<- read.table("2_Fin_Fol_ggplot.txt", h=T)
Fin_Rre_gg<- read.table("3_Fin_Rre_ggplot.txt", h=T)
Fin_Prh_gg <- read.table("4_Fin_Prh_ggplot.txt", h=T)
Fol_Poc_gg <- read.table("5_Poc_Fol_ggplot.txt", h=T)
Poc_Rre_gg <- read.table("6_Poc_Rre_ggplot.txt", h=T)
Poc_Prh_gg <- read.table("7_Poc_Prh_ggplot.txt", h=T)
Fol_Rre_gg <- read.table("8_Fol_Rre_ggplot.txt", h=T)
Fol_Prh_gg <- read.table("9_Fol_Prh_ggplot.txt", h=T)
Rre_Prh_gg <- read.table("10_Rre_Prh_ggplot.txt", h=T)
# Bubble plot
Fin_Poc <-read.table("1_Fin_Poc.txt", h=T)
Fin_Fol <-read.table("2_Fin_Fol.txt", h=T)
Fin_Rre <-read.table("3_Fin_Rre.txt", h=T)
Fin_Prh <-read.table("4_Fin_Prh.txt", h=T)
Poc_Fol <-read.table("5_Poc_Fol.txt", h=T)
Poc_Rre <-read.table("6_Poc_Rre.txt", h=T)
Poc_Prh <-read.table("7_Poc_Prh.txt", h=T)
Fol_Rre <-read.table("8_Fol_Rre.txt", h=T)
Fol_Prh <-read.table("9_Fol_Prh.txt", h=T)
Rre_Prh <-read.table("10_Rre_Prh.txt", h=T)
#############################################################################
#############################################################################
#############################################################################
#############################################################################
# 1.0 Correlogram spline bivariate with function "spline.correlog"
# Faramea involucellata (Fin) X Paclicourea octocuspis (Poc)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fin")]
w<- ab[c("Poc")]
library(SoDA)
xy<-geoXY (x, y)
spline1 <- spline.correlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fin"],
ab.rel[,"Poc"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fin_poc<-as.data.frame(spline1$real)
ac_fin_poc<- as.matrix(spline1$boot$boot.summary$predicted$y)
spline1[["real"]]
ab_fin_poc <- spline1[["real"]]
ac_fin_poc <- as.matrix(spline3$boot$boot.summary$predicted$y)
write.table(ab_fin_poc, "C:/Users/asus/Desktop/spl_fin1.txt")
write.table(ac_fin_poc, "C:/Users/asus/Desktop/spl_fin2.txt")
#############################################################################
# Faramea involucellata (Fin) X Faramea oligahtha (Fol)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fin")]
w<- ab[c("Fol")]
library(SoDA)
xy<-geoXY (x, y)
spline2 <- spline.correlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fin"],
ab.rel[,"Fol"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fin_fol<-as.data.frame(spline2$real)
ac_fin_fol<- as.matrix(spline2$boot$boot.summary$predicted$y)
spline2[["real"]]
ab_fin_fol <- spline2[["real"]]
ac_fin_fol <- as.matrix(spline3$boot$boot.summary$predicted$y)
write.table(ab_fin_fol, "C:/Users/asus/Desktop/spl_fin1.txt")
write.table(ac_fin_fol, "C:/Users/asus/Desktop/spl_fin2.txt")
#############################################################################
# Faramea involucellata (Fin) X Rudgea reflexa (Rre)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fin")]
w<- ab[c("Rre")]
library(SoDA)
xy<-geoXY (x, y)
spline3 <- spline.correlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fin"],
ab.rel[,"Rre"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fin_rre<-as.data.frame(spline3$real)
ac_fin_rre<- as.matrix(spline3$boot$boot.summary$predicted$y)
spline3[["real"]]
ab_fin_rre <- spline3[["real"]]
ac_fin_rre <- as.matrix(spline3$boot$boot.summary$predicted$y)
write.table(ab_fin_rre, "C:/Users/asus/Desktop/spl_fin1.txt")
write.table(ac_fin_rre, "C:/Users/asus/Desktop/spl_fin2.txt")
#############################################################################
# Faramea involucellata (Fin) X Psychotria rhytidocarpa (Prh)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fin")]
w<- ab[c("Prh")]
library(SoDA)
xy<-geoXY (x, y)
spline4 <- spline.coprhlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fin"],
ab.rel[,"Prh"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fin_prh<-as.data.frame(spline4$real)
ac_fin_prh<- as.matrix(spline4$boot$boot.summary$predicted$y)
spline4[["real"]]
ab_fin_prh <- spline4[["real"]]
ac_fin_prh <- as.matrix(spline4$boot$boot.summary$predicted$y)
write.table(ab_fin_prh, "C:/Users/asus/Desktop/spl_fin1.txt")
write.table(ac_fin_prh, "C:/Users/asus/Desktop/spl_fin2.txt")
#############################################################################
# Palicourea octocuspis (Poc) X Faramea oligantha (Fol)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Poc")]
w<- ab[c("Fol")]
library(SoDA)
xy<-geoXY (x, y)
spline5 <- spline.cofollog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Poc"],
ab.rel[,"Fol"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_poc_fol<-as.data.frame(spline5$real)
ac_poc_fol<- as.matrix(spline5$boot$boot.summary$predicted$y)
spline5[["real"]]
ab_poc_fol <- spline5[["real"]]
ac_poc_fol <- as.matrix(spline5$boot$boot.summary$predicted$y)
write.table(ab_poc_fol, "C:/Users/asus/Desktop/spl_poc_fol1.txt")
write.table(ac_poc_fol, "C:/Users/asus/Desktop/spl_poc_fol2.txt")
#############################################################################
# Palicourea octocuspis (Poc) X Rudgea reflexa (Rre)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Poc")]
w<- ab[c("Rre")]
library(SoDA)
xy<-geoXY (x, y)
spline6 <- spline.correlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Poc"],
ab.rel[,"Rre"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_poc_rre<-as.data.frame(spline6$real)
ac_poc_rre<- as.matrix(spline6$boot$boot.summary$predicted$y)
spline6[["real"]]
ab_poc_rre <- spline6[["real"]]
ac_poc_rre <- as.matrix(spline6$boot$boot.summary$predicted$y)
write.table(ab_poc_rre, "C:/Users/asus/Desktop/spl_poc_rre1.txt")
write.table(ac_poc_rre, "C:/Users/asus/Desktop/spl_poc_rre2.txt")
#############################################################################
# Palicourea octocuspis (Poc) X Psychotria rhytidocarpa (Prh)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Poc")]
w<- ab[c("Prh")]
library(SoDA)
xy<-geoXY (x, y)
spline7 <- spline.coprhlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Poc"],
ab.rel[,"Prh"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_poc_prh<-as.data.frame(spline7$real)
ac_poc_prh<- as.matrix(spline7$boot$boot.summary$predicted$y)
spline7[["real"]]
ab_poc_prh <- spline7[["real"]]
ac_poc_prh <- as.matrix(spline7$boot$boot.summary$predicted$y)
write.table(ab_poc_prh, "C:/Users/asus/Desktop/spl_poc_prh1.txt")
write.table(ac_poc_prh, "C:/Users/asus/Desktop/spl_poc_prh2.txt")
#############################################################################
# Faramea oligantha (Fol) X Rudgea reflexa (Rre)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fol")]
w<- ab[c("Prh")]
library(SoDA)
xy<-geoXY (x, y)
spline8 <- spline.coprhlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fol"],
ab.rel[,"Rre"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fol_prh<-as.data.frame(spline8$real)
ac_fol_prh<- as.matrix(spline8$boot$boot.summary$predicted$y)
spline8[["real"]]
ab_fol_prh <- spline8[["real"]]
ac_fol_prh <- as.matrix(spline8$boot$boot.summary$predicted$y)
write.table(ab_fol_prh, "C:/Users/asus/Desktop/spl_fol_rre1.txt")
write.table(ac_fol_prh, "C:/Users/asus/Desktop/spl_fol_rre2.txt")
#############################################################################
# Faramea oligantha (Fol) X Psychotria rhytidocarpa (Prh)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Fol")]
w<- ab[c("Prh")]
library(SoDA)
xy<-geoXY (x, y)
spline9 <- spline.coprhlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Fol"],
ab.rel[,"Prh"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_fol_prh<-as.data.frame(spline9$real)
ac_fol_prh<- as.matrix(spline9$boot$boot.summary$predicted$y)
spline9[["real"]]
ab_fol_prh <- spline9[["real"]]
ac_fol_prh <- as.matrix(spline9$boot$boot.summary$predicted$y)
write.table(ab_fol_prh, "C:/Users/asus/Desktop/spl_fol_prh1.txt")
write.table(ac_fol_prh, "C:/Users/asus/Desktop/spl_fol_prh2.txt")
#############################################################################
# Rudgea reflexa (Rre) X Psychotria rhytidocarpa (Prh)
x<- xy[,"x"]
y<- xy[,"y"]
w<- ab[c("Rre")]
w<- ab[c("Prh")]
library(SoDA)
xy<-geoXY (x, y)
spline10 <- spline.coprhlog(xy[,"X"],
xy[,"Y"],
ab.rel[,"Rre"],
ab.rel[,"Prh"],
resamp=10000,
latlon=FALSE,
npoints = 203)
ab_rre_prh<-as.data.frame(spline10$real)
ac_rre_prh<- as.matrix(spline10$boot$boot.summary$predicted$y)
spline10[["real"]]
ab_rre_prh <- spline10[["real"]]
ac_rre_prh <- as.matrix(spline10$boot$boot.summary$predicted$y)
write.table(ab_rre_prh, "C:/Users/asus/Desktop/spl_rre_prh1.txt")
write.table(ac_rre_prh, "C:/Users/asus/Desktop/spl_rre_prh2.txt")
#############################################################################
#############################################################################
#############################################################################
#############################################################################
# 2.0 Correlogram spline bivariate with ggplot2
p1<-ggplot(Fin_Poc_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 1, size = 12))+
geom_ribbon(aes(ymin=a, ymax=b),fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p1
p1<- p1 +
xlab(paste("Distance")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p1
p1 <- p1 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p1
p1<- p1+ theme(text=element_text(size=12,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p1
#############################################################################
p2<-ggplot(Fin_Fol_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p2
p2<- p2 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p2
p2 <- p2 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p2
p2<- p2+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p2
#############################################################################
p3<-ggplot(Fin_Rre_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p3
p3<- p3 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p3
p3 <- p3 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p3
p3<- p3+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p3
#############################################################################
p4 <-ggplot(Fin_Prh_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p4
p4<- p4 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p4
p4 <- p4 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p4
p4<- p4+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p4
#############################################################################
p5 <-ggplot(Fol_Poc_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p5
p5<- p5 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p5
p5 <- p5 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p5
p5<- p5+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p5
#############################################################################
p6 <-ggplot(Poc_Rre_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p6
p6 <- p6 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p6
p6 <- p6 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p6
p6 <- p6+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p6
#############################################################################
p7 <-ggplot(Poc_Prh_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p7
p7 <- p7 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p7
p7 <- p7 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p7
p7 <- p7+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p7
#############################################################################
p8 <-ggplot(Fol_Rre_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p8
p8 <- p8 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p8
p8 <- p8 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p8
p8 <- p8+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p8
#############################################################################
p9 <-ggplot(Fol_Prh_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p9
p9 <- p9 +
xlab(paste(" ")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p9
p9 <- p9 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p9
p9 <- p9+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p9
#############################################################################
p10 <-ggplot(Rre_Prh_gg, aes(d,a)) +
scale_x_continuous(limits=c(0,300)) +
expand_limits(y=c(-1,1)) +
scale_y_continuous(limits=c(-1,1)) +
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.grid.minor = element_line(colour = NULL),
panel.grid.major = element_line(colour = NULL),
plot.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
axis.text.x = element_text(color ="black", size = 12, angle = 0),
axis.text.y = element_text(color ="black", size = 12, angle = 0),
plot.title = element_text(hjust = 0.5, size = 15))+
geom_ribbon(aes(ymin=a, ymax=b), fill = "#6a6a6a")+
geom_smooth(stat="identity",fill="grey",colour="white")+
geom_line(aes(y=y))
p10
p10 <- p10 +
xlab(paste("Distance (m)")) +
theme(axis.title.x=element_text(angle = 0, size = 15)) + #, face = "bold"
ylab(paste("Correlation")) +
theme(axis.title.y=element_text(angle = 90, size = 15)) #, face = "bold"
p10
p10 <- p10 +
geom_hline(yintercept=0)
#labs(title = expression(paste(italic("Nome da esp?cie"))))
p10
p10 <- p10+ theme(text=element_text(size=16,
# family="Comic Sans MS"))
# family="CM Roman"))
# family="TT Times New Roman"))
# family="Sans"))
family="TT Times New Roman"))
p10
#############################################################################
tiff(filename="Bivariate.tiff", res=300, height=900/72*500, width=100/72*800, compression= "lzw")
# simple grid with labels and aligned plots
plot_grid(p1, p2, p3, p4, p5,
p6, p7, p8, p9, p10,
labels = c("A", "B", "C", "D", "E",
"F", "G", "H", "I", "J"),
ncol = 1)
dev.off()
#############################################################################
#############################################################################
#############################################################################
#############################################################################
# 3.0 Bubble plot for bivariate spatial correlograms of the five most abundant species
b1 <- ggplot(Fin_Poc, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
geom_count() +
scale_size_area()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b1
angulo=-0.65
xnew_Fin_Poc <- Fin_Poc[,"x"]*cos(angulo) + Fin_Poc[,"y"]*sin(angulo)
ynew_Fin_Poc <- -Fin_Poc[,"x"]*sin(angulo) + Fin_Poc[,"y"]*cos(angulo)
b1 <- ggplot(Fin_Poc, aes(x=xnew_Fin_Poc, y=ynew_Fin_Poc, size = Abundance, colour = Species)) +
scale_x_continuous(limits=c(-20.298, -20.292))+
scale_y_continuous(limits=c(-41.3245, -41.3230))+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9)+
geom_count() +
scale_size_area()+
#ggtitle("Faramea involucellata X Faramea campanella") +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b1
b1 <- b1 + coord_fixed(ratio = -0.81)
b1
b1 <- b1 +labs(title="", x=" ", y = "Longitude")
b1
#############################################################################
b2 <- ggplot(Fin_Fol, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b2
angulo=-0.65
xnew_Fin_Fol <- Fin_Fol[,"x"]*cos(angulo) + Fin_Fol[,"y"]*sin(angulo)
ynew_Fin_Fol <- -Fin_Fol[,"x"]*sin(angulo) + Fin_Fol[,"y"]*cos(angulo)
b2 <- ggplot(Fin_Fol, aes(x=xnew_Fin_Fol, y=ynew_Fin_Fol, size = Abundance, colour = Species)) +
scale_x_continuous(limits=c(-20.298, -20.292))+
scale_y_continuous(limits=c(-41.3245, -41.3230))+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
#ggtitle("Faramea involucellata X Faramea campanella") +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b2
b2 <- b2 + coord_fixed(ratio = -0.81)
b2
b2 <- b2 +labs(title="", x=" ", y = "Longitude")
b2
b2 <- b2 + guides(color = guide_legend(order=2),
size = guide_legend(order=1))
#shape = guide_legend(order=3))
b2
###########################################################################
b3 <- ggplot(Fin_Rre, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b3
angulo=-0.65
xnew_Fin_Rre <- Fin_Rre[,"x"]*cos(angulo) + Fin_Rre[,"y"]*sin(angulo)
ynew_Fin_Rre <- -Fin_Rre[,"x"]*sin(angulo) + Fin_Rre[,"y"]*cos(angulo)
b3 <- ggplot(Fin_Rre, aes(x=xnew_Fin_Rre, y=ynew_Fin_Rre, size = Abundance, colour = Species)) +
scale_x_continuous(limits=c(-20.298, -20.292))+
scale_y_continuous(limits=c(-41.3245, -41.3230))+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
#ggtitle("Faramea involucellata X Faramea campanella") +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b3
b3 <- b3 + coord_fixed(ratio = -0.81)
b3
b3 <- b3 +labs(title="", x=" ", y = "Longitude")
b3
###########################################################################
b4 <- ggplot(Fin_Prh, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b4
#Alterando o ?ngulo
angulo=-0.65
xnew_Fin_Prh <- Fin_Prh[,"x"]*cos(angulo) + Fin_Prh[,"y"]*sin(angulo)
ynew_Fin_Prh <- -Fin_Prh[,"x"]*sin(angulo) + Fin_Prh[,"y"]*cos(angulo)
b4 <- ggplot(Fin_Prh, aes(x=xnew_Fin_Prh, y=ynew_Fin_Prh, size = Abundance, colour = Species)) +
scale_x_continuous(limits=c(-20.298, -20.292))+
scale_y_continuous(limits=c(-41.3245, -41.3230))+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
#ggtitle("Faramea involucellata X Faramea campanella") +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b4
b4 <- b4 + coord_fixed(ratio = -0.81)
b4
b4 <- b4 +labs(title="", x=" ", y = "Longitude")
b4
###########################################################################
b5 <- ggplot(Poc_Fol, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b5
angulo=-0.65
xnew_Poc_Fol <- Poc_Fol[,"x"]*cos(angulo) + Poc_Fol[,"y"]*sin(angulo)
ynew_Poc_Fol <- -Poc_Fol[,"x"]*sin(angulo) + Poc_Fol[,"y"]*cos(angulo)
b5 <- ggplot(Poc_Fol, aes(x=xnew_Poc_Fol, y=ynew_Poc_Fol, size = Abundance, colour = Species)) +
scale_x_continuous(limits=c(-20.298, -20.292))+
scale_y_continuous(limits=c(-41.3245, -41.3230))+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
#ggtitle("Faramea involucellata X Faramea campanella") +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b5
b5 <- b5 + coord_fixed(ratio = -0.81)
b5
b5 <- b5 +labs(title="", x=" ", y = "Longitude")
b5
###########################################################################
b6 <- ggplot(Poc_Rre, aes(x=x, y=y, size = Abundance, colour = Species)) +
scale_fill_viridis()+
scale_colour_manual(values = c("Black", "Grey"))+
geom_point(alpha=0.9) +
theme_bw() +
theme(text=element_text(family="Times", face="plain", size=20))+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
b6
angulo=-0.65
xnew_Poc_Rre <- Poc_Rre[,"x"]*cos(angulo) + Poc_Rre[,"y"]*sin(angulo)
ynew_Poc_Rre <- -Poc_Rre[,"x"]*sin(angulo) + Poc_Rre[,"y"]*cos(angulo)