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PlotVariations<- function(shapes,reference,path,save=F, w = 6, h = 6, d = 100, c_ref="red", c_target="black", s_ref=3, s_target=2){
x<-y<-xmin<-ymin<-xmax<-ymax<-NULL
if (!(is.list(shapes)))
{stop("Shapes must be list type")}
if (!(is.matrix(reference)))
{stop("Reference landmarks must be matrix type")}
if (length(shapes[[1]])!=length(reference))
{stop("Shapes and reference must be the same length")}
ref<-data.frame(x=reference[,1], y=reference[,2])
#Calculate min and max values for reference
xmin<-min(ref$x)
xmax<-max(ref$x)
ymin<-min(ref$y)
ymax<-max(ref$y)
newplots<-list()
for(i in 1:length(shapes)){
ext<-shapes[[i]]
vari<-data.frame(x=ext[,1], y=ext[,2])
ti<-paste("Target No.", i)
newplots[[i]]<-ggplot(data=ref,aes(x=x,y=y))+
geom_point(size=s_ref, color=c_ref)+coord_fixed()+
geom_point(data=vari,aes(x=x,y=y),color=c_target,size=s_target)+
geom_segment(data=vari,aes(x = x, y = y, xend = ref$x, yend = ref$y),show.legend = T)+
theme_bw()+ggtitle(ti)+xlab("")+ylab("")+
theme(axis.text=element_blank(), axis.ticks=element_blank())
#Calculate max and min scale
if(min(vari$x)<xmin){xmin<-min(vari$x)}
if(max(vari$x)>xmax){xmax<-max(vari$x)}
if(min(vari$y)<ymin){ymin<-min(vari$y)}
if(max(vari$y)>ymax){ymax<-max(vari$y)}
}
for (i in 1:length(newplots)){newplots[[i]]<-newplots[[i]]+xlim(xmin,xmax)+ylim(ymin,ymax)}
if (save==T){
if (missing(path))
{time=format(Sys.time(),"%a_%H_%M")
path <- file.path(getwd(),time)
print("Path not provided. Default path created on current working directory")
dir.create(path)}
for(g in 1:length(shapes)){
if(g<10){ggsave(paste(path,"/model","000",g, ".jpeg", sep = ""),plot=newplots[[g]], width = h, height = w, units = 'in', dpi = d)}
if(g<100 && g>=10){ggsave(paste(path,"/model","00",g, ".jpeg", sep = ""),plot=newplots[[g]], width = h, height = w, units = 'in', dpi = d)}
if(g>=100){ggsave(paste(path,"/model","00",g, ".jpeg", sep = ""),plot=newplots[[g]], width = h, height = w, units = 'in', dpi = d)}
}
}
return (newplots)
}
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