R/Main_Figures.R
In ZacharySMorris/Morris-Chapter2Code: This package contains all of the code and necessary raw data for chapter 2 of my disseration (Morris, 2020)
###Main Figures for Chapter 2###
###Figure 1###
##Panel A - Extant only on total morphospace
#Generate Plot#
PCA <- Combined_CrocDorsal.pca
PV <- Combined_CrocDorsal.PlottingValues
Xlim<-c(floor(min(PCA$pc.scores[,1])*10)/10,ceiling(max(PCA$pc.scores[,1])*10)/10)
Ylim<-c(floor(min(PCA$pc.scores[,2])*10)/10,ceiling(max(PCA$pc.scores[,2])*10)/10)
pdf("Crocodylia_Extant_Ontogeny_on_Combined_Morphospace.pdf",11,8.5,useDingbats = FALSE)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Principal Component 1 (", round(100*PCA$pc.summary$importance[2,"PC1"], digits = 1), "%)", sep = ""),
ylab = paste("Principal Component 2 (", round(100*PCA$pc.summary$importance[2,"PC2"], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2],by=0.1),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
abline(v=0, lty=3)
clip(-0.4,0.4,-0.4,0.4)
points(PCA$pc.scores[grep("Extant", classifier$Extant),1], PCA$pc.scores[grep("Extant", classifier$Extant),2],
pch=PV$shape[grep("Extant", classifier$Extant)],
cex=PV$size[grep("Extant", classifier$Extant)],
bg=alpha(PV$color[grep("Extant", classifier$Extant)], 0.75), asp=F)
legend(-0.275, 0.2, Crocodylia_Ecomorphs$taxa,
cex = 1,
fill = alpha(Crocodylia_Ecomorphs$legendcolor, 0.75),
bty = "n",
horiz = TRUE)
legend(-0.275, 0.18, c("Alligatoridae", "Crocodylidae", "Gavialis", "Tomistoma"),
cex = 1,
pch = Crocodylia_Ecomorphs$legendshape,
pt.bg = "black",
pt.cex = 1.5,
bty = "n",
horiz = TRUE)
dev.off()
plot.major.axis(Clades2.MajorAxis.Slopes,Fossil_Morphospace_Clades2$PCvalues,Combined_CrocDorsal.pca,c(1,3))
##Panel B - Major Axes of ontogeny and Adult Ecology
Subset_data <- Adult_Ecomorphs
i='Crocodylia'
PCs <- c(1,2)
ConfIntList <- Adult_Total_Morphospace.MajorAxis_1
MA_number <- Adult_Total_Morphospace.MajorAxis_1$MA_number
LineColor <- unique(Adult_Ecomorphs$color$Crocodylia)
Xlim<-c(floor(min(PCA$pc.scores[,1])*10)/10,ceiling(max(PCA$pc.scores[,1])*10)/10)
Ylim<-c(floor(min(PCA$pc.scores[,2])*10)/10,ceiling(max(PCA$pc.scores[,2])*10)/10)
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs$legendcolor, OnePlot=TRUE)
clip(-0.4,0.4,-0.4,0.4)
polygon(c(rev(ConfIntList$NEW_Xs[[i]]), ConfIntList$NEW_Xs[[i]]),
c(rev(ConfIntList$preds_CIupper[[i]]), ConfIntList$preds_CIlower[[i]]),
col = alpha('grey',0.6), border = NA)
clip(
min(ConfIntList$NEW_Xs[[i]]),
max(ConfIntList$NEW_Xs[[i]]),
min(ConfIntList$preds_CIlower[[i]]),
max(ConfIntList$preds_CIupper[[i]])
)
lines(ConfIntList$NEW_Xs[[i]], ConfIntList$preds_CIlower[[i]], lty = 'dashed', col = LineColor)
lines(ConfIntList$NEW_Xs[[i]], ConfIntList$preds_CIupper[[i]], lty = 'dashed', col = LineColor)
abline(ConfIntList$Intercept_list[[i]][MA_number],ConfIntList$Slope_list[[i]][MA_number], col = LineColor, lwd=3, lty=1 )
dataEllipse(Subset_data$PCvalues[[i]][,PCs[1]],
Subset_data$PCvalues[[i]][,PCs[2]],
add = TRUE, plot.points = FALSE, levels = c(0.75),
col = LineColor, fill = FALSE)
dev.off()
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes_G_T_Unique.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs_G_T_Unique, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_G_T_Unique_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs_G_T_Unique$legendcolor, OnePlot=TRUE)
dev.off()
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes_No_ExtremeGroups.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs_Non_Extreme, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_Non_Extreme_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs_Non_Extreme$legendcolor, OnePlot=TRUE)
dev.off()
###
###Figure 2###
##Panel A - All Crocodylomorph Fossils on Extant Major Axes
##Panel B - Sub-plots of distinct clades
#Basal Pseudosuchians
#"Spehnosuchians"
#Thalattosuchians
#Notosuchians
#Protosuchians
#Tethysuchians
#Gonipholids
###Allometric Plots###
GPA <- Combined_CrocDorsal.gpa
PCA <- Combined_CrocDorsal.pca
Subset_Groups <- Combined_Morphospace_Clades3
PC_Y <- 2
for(i in 1:length(Subset_Groups$taxa)){
CS_log <- log(Subset_Groups$CSize[[i]])
PCScores <- Subset_Groups$PCvalues[[i]]
PV_color <- Subset_Groups$color[[i]]
PV_size <- Subset_Groups$size[[i]]
PV_shape <- Subset_Groups$shape[[i]]
Xlim<-c(0,ceiling(max(log(GPA$Csize))))
Ylim<-c(floor(min(PCA$pc.scores[,PC_Y])*10)/10,ceiling(max(PCA$pc.scores[,PC_Y])*10)/10)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Centroid Size (log scale)"),
ylab = paste("Principal Component ", PC_Y, " (", round(100*PCA$pc.summary$importance[2, PC_Y], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2]),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
clip(0,Xlim[2],-0.4,0.4)
points(CS_log, PCScores[,1],
pch=PV_shape,
cex=PV_size,
bg=alpha(PV_color, 0.75), asp=F)
mtext(Subset_Groups$taxa[[i]])
}
CS_log <- log(Combined_CrocDorsal.gpa$Csize)
sapply(Combined_CrocDorsal.gpa$coords, "dist")
Combined_HeadLengh <- c()
for(i in 1:length(Combined_CrocDorsal.gpa$Csize)){
temp_dist <- dist(combined_CrocDorsal[,,i][c(1,4),])
Combined_HeadLengh <- append(Combined_HeadLengh, temp_dist)
}
PCA <- Combined_CrocDorsal.pca
PV <- Combined_CrocDorsal.PlottingValues
PC_Y <- 1
Xlim<-c(0,ceiling(max(CS_log)))
Ylim<-c(floor(min(PCA$pc.scores[,PC_Y])*10)/10,ceiling(max(PCA$pc.scores[,PC_Y])*10)/10)
# pdf("Crocodylia_Extant_Ontogeny_on_Combined_Morphospace.pdf",11,8.5,useDingbats = FALSE)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Centroid Size (log scale)"),
ylab = paste("Principal Component ", PC_Y, " (", round(100*PCA$pc.summary$importance[2, PC_Y], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2]),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
clip(0,Xlim[2],-0.4,0.4)
points(CS_log[grep("Extant", classifier$Extant)], PCA$pc.scores[grep("Extant", classifier$Extant),1],
pch=PV$shape[grep("Extant", classifier$Extant)],
cex=PV$size[grep("Extant", classifier$Extant)],
bg=alpha(PV$color[grep("Extant", classifier$Extant)], 0.75), asp=F)
points(CS_log[grep("Fossil", classifier$Extant)], PCA$pc.scores[grep("Fossil", classifier$Extant),1],
pch=PV$shape[grep("Fossil", classifier$Extant)],
cex=PV$size[grep("Fossil", classifier$Extant)],
bg=alpha(PV$color[grep("Fossil", classifier$Extant)], 0.75), asp=F)
text(CS_log[grep("Extant", classifier$Extant)], PCA$pc.scores[grep("Extant", classifier$Extant),1],
names(Combined_CrocDorsal.gpa$Csize)[grep("Extant", classifier$Extant)])
log(Combined_CrocDorsal.gpa$Csize)[grep("osteolaemus osborni", names(Combined_CrocDorsal.gpa$Csize))]
classifier$image[grep("osteolaemus osborni", names(Combined_CrocDorsal.gpa$Csize))]
points(CS_log, PCA[,1],
pch=PV_shape,
cex=PV_size,
bg=alpha(PV_color, 0.75), asp=F)
plot(Combined_HeadLengh[grep("Fossil", classifier$Extant)], Combined_CrocDorsal.gpa$Csize[grep("Fossil", classifier$Extant)],
pch=PV$shape[grep("Fossil", classifier$Extant)],
cex=PV$size[grep("Fossil", classifier$Extant)],
bg=alpha(PV$color[grep("Fossil", classifier$Extant)], 0.75), asp=F)
plot(Combined_HeadLengh, Combined_CrocDorsal.gpa$Csize,
pch=PV$shape,
cex=PV$size,
bg=alpha(PV$color, 0.75), asp=F)
plot(log(Combined_HeadLengh), PCA$pc.scores[,1],
pch=PV$shape,
cex=PV$size,
bg=alpha(PV$color, 0.75), asp=F)
ZacharySMorris/Morris-Chapter2Code documentation built on Sept. 5, 2020, 12:53 a.m.
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###Main Figures for Chapter 2###
###Figure 1###
##Panel A - Extant only on total morphospace
#Generate Plot#
PCA <- Combined_CrocDorsal.pca
PV <- Combined_CrocDorsal.PlottingValues
Xlim<-c(floor(min(PCA$pc.scores[,1])*10)/10,ceiling(max(PCA$pc.scores[,1])*10)/10)
Ylim<-c(floor(min(PCA$pc.scores[,2])*10)/10,ceiling(max(PCA$pc.scores[,2])*10)/10)
pdf("Crocodylia_Extant_Ontogeny_on_Combined_Morphospace.pdf",11,8.5,useDingbats = FALSE)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Principal Component 1 (", round(100*PCA$pc.summary$importance[2,"PC1"], digits = 1), "%)", sep = ""),
ylab = paste("Principal Component 2 (", round(100*PCA$pc.summary$importance[2,"PC2"], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2],by=0.1),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
abline(v=0, lty=3)
clip(-0.4,0.4,-0.4,0.4)
points(PCA$pc.scores[grep("Extant", classifier$Extant),1], PCA$pc.scores[grep("Extant", classifier$Extant),2],
pch=PV$shape[grep("Extant", classifier$Extant)],
cex=PV$size[grep("Extant", classifier$Extant)],
bg=alpha(PV$color[grep("Extant", classifier$Extant)], 0.75), asp=F)
legend(-0.275, 0.2, Crocodylia_Ecomorphs$taxa,
cex = 1,
fill = alpha(Crocodylia_Ecomorphs$legendcolor, 0.75),
bty = "n",
horiz = TRUE)
legend(-0.275, 0.18, c("Alligatoridae", "Crocodylidae", "Gavialis", "Tomistoma"),
cex = 1,
pch = Crocodylia_Ecomorphs$legendshape,
pt.bg = "black",
pt.cex = 1.5,
bty = "n",
horiz = TRUE)
dev.off()
plot.major.axis(Clades2.MajorAxis.Slopes,Fossil_Morphospace_Clades2$PCvalues,Combined_CrocDorsal.pca,c(1,3))
##Panel B - Major Axes of ontogeny and Adult Ecology
Subset_data <- Adult_Ecomorphs
i='Crocodylia'
PCs <- c(1,2)
ConfIntList <- Adult_Total_Morphospace.MajorAxis_1
MA_number <- Adult_Total_Morphospace.MajorAxis_1$MA_number
LineColor <- unique(Adult_Ecomorphs$color$Crocodylia)
Xlim<-c(floor(min(PCA$pc.scores[,1])*10)/10,ceiling(max(PCA$pc.scores[,1])*10)/10)
Ylim<-c(floor(min(PCA$pc.scores[,2])*10)/10,ceiling(max(PCA$pc.scores[,2])*10)/10)
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs$legendcolor, OnePlot=TRUE)
clip(-0.4,0.4,-0.4,0.4)
polygon(c(rev(ConfIntList$NEW_Xs[[i]]), ConfIntList$NEW_Xs[[i]]),
c(rev(ConfIntList$preds_CIupper[[i]]), ConfIntList$preds_CIlower[[i]]),
col = alpha('grey',0.6), border = NA)
clip(
min(ConfIntList$NEW_Xs[[i]]),
max(ConfIntList$NEW_Xs[[i]]),
min(ConfIntList$preds_CIlower[[i]]),
max(ConfIntList$preds_CIupper[[i]])
)
lines(ConfIntList$NEW_Xs[[i]], ConfIntList$preds_CIlower[[i]], lty = 'dashed', col = LineColor)
lines(ConfIntList$NEW_Xs[[i]], ConfIntList$preds_CIupper[[i]], lty = 'dashed', col = LineColor)
abline(ConfIntList$Intercept_list[[i]][MA_number],ConfIntList$Slope_list[[i]][MA_number], col = LineColor, lwd=3, lty=1 )
dataEllipse(Subset_data$PCvalues[[i]][,PCs[1]],
Subset_data$PCvalues[[i]][,PCs[2]],
add = TRUE, plot.points = FALSE, levels = c(0.75),
col = LineColor, fill = FALSE)
dev.off()
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes_G_T_Unique.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs_G_T_Unique, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_G_T_Unique_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs_G_T_Unique$legendcolor, OnePlot=TRUE)
dev.off()
pdf("Crocodylia_Ontogny_and_Ecology_MajorAxes_No_ExtremeGroups.pdf",11,8.5,useDingbats = FALSE)
CI_Poly_Plot(Crocodylia_Ecomorphs_Non_Extreme, Combined_CrocDorsal.pca, Crocodylia_Ecomorphs_Non_Extreme_Total_Morphospace.MajorAxis_1, Crocodylia_Ecomorphs_Non_Extreme$legendcolor, OnePlot=TRUE)
dev.off()
###
###Figure 2###
##Panel A - All Crocodylomorph Fossils on Extant Major Axes
##Panel B - Sub-plots of distinct clades
#Basal Pseudosuchians
#"Spehnosuchians"
#Thalattosuchians
#Notosuchians
#Protosuchians
#Tethysuchians
#Gonipholids
###Allometric Plots###
GPA <- Combined_CrocDorsal.gpa
PCA <- Combined_CrocDorsal.pca
Subset_Groups <- Combined_Morphospace_Clades3
PC_Y <- 2
for(i in 1:length(Subset_Groups$taxa)){
CS_log <- log(Subset_Groups$CSize[[i]])
PCScores <- Subset_Groups$PCvalues[[i]]
PV_color <- Subset_Groups$color[[i]]
PV_size <- Subset_Groups$size[[i]]
PV_shape <- Subset_Groups$shape[[i]]
Xlim<-c(0,ceiling(max(log(GPA$Csize))))
Ylim<-c(floor(min(PCA$pc.scores[,PC_Y])*10)/10,ceiling(max(PCA$pc.scores[,PC_Y])*10)/10)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Centroid Size (log scale)"),
ylab = paste("Principal Component ", PC_Y, " (", round(100*PCA$pc.summary$importance[2, PC_Y], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2]),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
clip(0,Xlim[2],-0.4,0.4)
points(CS_log, PCScores[,1],
pch=PV_shape,
cex=PV_size,
bg=alpha(PV_color, 0.75), asp=F)
mtext(Subset_Groups$taxa[[i]])
}
CS_log <- log(Combined_CrocDorsal.gpa$Csize)
sapply(Combined_CrocDorsal.gpa$coords, "dist")
Combined_HeadLengh <- c()
for(i in 1:length(Combined_CrocDorsal.gpa$Csize)){
temp_dist <- dist(combined_CrocDorsal[,,i][c(1,4),])
Combined_HeadLengh <- append(Combined_HeadLengh, temp_dist)
}
PCA <- Combined_CrocDorsal.pca
PV <- Combined_CrocDorsal.PlottingValues
PC_Y <- 1
Xlim<-c(0,ceiling(max(CS_log)))
Ylim<-c(floor(min(PCA$pc.scores[,PC_Y])*10)/10,ceiling(max(PCA$pc.scores[,PC_Y])*10)/10)
# pdf("Crocodylia_Extant_Ontogeny_on_Combined_Morphospace.pdf",11,8.5,useDingbats = FALSE)
plot(0, 0, type = "n",
xlim = Xlim,
ylim = Ylim,
xlab = paste("Centroid Size (log scale)"),
ylab = paste("Principal Component ", PC_Y, " (", round(100*PCA$pc.summary$importance[2, PC_Y], digits = 1), "%)", sep = ""),
axes = FALSE,
frame.plot = FALSE,
asp=F)
axis(1, round(seq(Xlim[1],Xlim[2]),1), pos=Ylim[1])
axis(2, round(seq(Ylim[1],Ylim[2],by=0.1),1), pos=Xlim[1], las = 1)
clip(Xlim[1],Xlim[2],Ylim[1],Ylim[2])
abline(h=0, lty=3)
clip(0,Xlim[2],-0.4,0.4)
points(CS_log[grep("Extant", classifier$Extant)], PCA$pc.scores[grep("Extant", classifier$Extant),1],
pch=PV$shape[grep("Extant", classifier$Extant)],
cex=PV$size[grep("Extant", classifier$Extant)],
bg=alpha(PV$color[grep("Extant", classifier$Extant)], 0.75), asp=F)
points(CS_log[grep("Fossil", classifier$Extant)], PCA$pc.scores[grep("Fossil", classifier$Extant),1],
pch=PV$shape[grep("Fossil", classifier$Extant)],
cex=PV$size[grep("Fossil", classifier$Extant)],
bg=alpha(PV$color[grep("Fossil", classifier$Extant)], 0.75), asp=F)
text(CS_log[grep("Extant", classifier$Extant)], PCA$pc.scores[grep("Extant", classifier$Extant),1],
names(Combined_CrocDorsal.gpa$Csize)[grep("Extant", classifier$Extant)])
log(Combined_CrocDorsal.gpa$Csize)[grep("osteolaemus osborni", names(Combined_CrocDorsal.gpa$Csize))]
classifier$image[grep("osteolaemus osborni", names(Combined_CrocDorsal.gpa$Csize))]
points(CS_log, PCA[,1],
pch=PV_shape,
cex=PV_size,
bg=alpha(PV_color, 0.75), asp=F)
plot(Combined_HeadLengh[grep("Fossil", classifier$Extant)], Combined_CrocDorsal.gpa$Csize[grep("Fossil", classifier$Extant)],
pch=PV$shape[grep("Fossil", classifier$Extant)],
cex=PV$size[grep("Fossil", classifier$Extant)],
bg=alpha(PV$color[grep("Fossil", classifier$Extant)], 0.75), asp=F)
plot(Combined_HeadLengh, Combined_CrocDorsal.gpa$Csize,
pch=PV$shape,
cex=PV$size,
bg=alpha(PV$color, 0.75), asp=F)
plot(log(Combined_HeadLengh), PCA$pc.scores[,1],
pch=PV$shape,
cex=PV$size,
bg=alpha(PV$color, 0.75), asp=F)
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