mesonplot.R

##this will turn matlab output into a pretty graph without having to think about it.
# install.packages(c("Cairo"), repos="http://cran.r-project.org" )
library(Cairo)
library(plyr)
library(ggplot2)
library(grid)
source("C:/Users/phug7649/Desktop/TXTBIN/R-scripts/functions/make_letter_ids.R")

##input files for matlab:

setwd("C:\\Users\\phug7649\\Documents\\MATLAB")
matrix<-read.table("matrix.csv",sep=",")
end_points<-read.csv("EP.csv",sep=",")
data<-read.csv("DATA.csv",sep=",")

##matlab output files:
centroid_table<-read.csv("mcent.csv",header=FALSE,sep=",")
a<-nrow(centroid_table)
y<-make_letter_ids(nrow(centroid_table))
centroid_table<-cbind(y,centroid_table)
##joining original data to the centroid table, to be used later.
names(centroid_table) <- names(data)
data_cent<-rbind(data,centroid_table)
##creating principal components from the original data.
princomp_main<-princomp(data_cent[,2:ncol(data)],cor=TRUE)
princomp_comp<-princomp_main$scores
##attaching principal components to main data, plotting to ensure we know what it looks like.
#plot(princomp_comp[,1],princomp_comp[,2])
##creating max distance column
data_distances<-read.csv("mdist.csv",sep=",",header=F)  
id.matrix<-diag(nrow(centroid_table))
max<-y
id.matrix<-cbind(id.matrix,max)
natural_key<-max
data_cent.prin<-cbind(data_cent,princomp_comp)



names(data_distances)<-make_letter_ids(nrow(centroid_table))
weighting_factor<-read.csv("weighting.csv",sep=",")
number_of_rows<-read.csv("rows.csv",header=FALSE,sep=",")
number_of_end_members<-read.csv("end.csv",header=FALSE,sep=",")
number_of_centroids<-read.csv("cent.csv",header=FALSE,sep=",")
w<-weighting_factor[1,1]

##create the id matrix from the matlab data


##creating max column for data distances
aa<-as.matrix(data_distances)
data_distances$max<-apply(aa,1,which.max)
data_ratio<-data_distances
data_ratio$max<-apply(aa,1,which.max)
max<-make_letter_ids(nrow(centroid_table))
data_distances$max<-max[data_distances$max]
max<-data_distances$max

max<-rbind(c(max,y))
max<-t(max)


data.complete<-cbind(data_cent.prin,max)
datarows<-nrow(data)
position1<-datarows+1
cdatarows<-nrow(data.complete)
centroids.complete<-data.complete[position1:cdatarows,]
emno<-number_of_end_members[1,1]
ceno<-nrow(centroid_table)-emno
soil.id<-rep(c("E", "C"), c(emno, ceno))
centroids.complete<-cbind(centroids.complete,soil.id)


totals<-as.data.frame(table(data_ratio$max))
end.tot<-totals[1:nrow(matrix),]
cent.tot<-totals[nrow(matrix):nrow(totals),]
sum.end<-sum(end.tot[,2])
sum.cent<-sum(cent.tot[,2])  
ratio<-(sum.end/(sum.end+sum.cent))*100
ratio<-round(ratio,digits=2)
message(paste0("Weighting ", weighting_factor[1,1],", creating ",ratio, "% end point memberships"))

setwd("C:/Users/phug7649/Desktop/txtbin")

###SEB GOING NUTS (more often referred to as a panel plot)
NUTS<-ggplot(data.complete, aes(x=Comp.1, y=Comp.2), group=max)+
  theme_bw() +
  geom_point(colour="grey40")+
  #stat_bin2d(binwidth=c(1, 1),colour=gray) +
  facet_wrap(~ max, nrow=5)+
  geom_point(data=centroids.complete, aes(shape=soil.id),size=4, colour="black")+  
  scale_shape_manual(values=c(16, 17))+
  theme(plot.background = element_rect(fill = w))+
#    xlim(-12,8)+
#    ylim(-7.5,5)+
  
  ggtitle(paste0("Weighting ", weighting_factor[1,1],", creating ",ratio, " percent end point memberships"))+
 # theme(panel.margin = unit(5, "lines"))+
  coord_equal()

NUTS

ggsave(paste0("nuts", w, number_of_end_members[1,1],".png"),type="cairo")



#Assign colours in one giant plot for Alex. 


#hclust(centroids.complete[,2:19])
#qplot(Comp.1,Comp.2,data=data.complete,colour=centroids.complete$soil.id)

combined<-ggplot(data.complete,aes(x=Comp.1,y=Comp.2))+
        geom_point(aes(colour=max))+
        geom_point(data=centroids.complete,aes(shape=soil.id),size=4)+
        scale_shape_manual(values=c(16,17))+
#         xlim(-12,8)+
#         ylim(-7.5,5)+
        ggtitle(paste0("Weighting ", weighting_factor[1,1],", creating ",ratio, " percent end point memberships"))+
        coord_equal()
combined
ggsave(paste0("combined", w, number_of_end_members[1,1],".png"),type="cairo")