# R Script authored by Daniel Pass, Cardiff University, UK # 3rd December 2013 # library(vegan) #Load data worm <-read.csv("/Users/normanmorrison/Desktop/Dan Pass/worm_gen_matrix_drop.csv", header=TRUE) worm.env <- read.csv("/Users/normanmorrison/Desktop/Dan Pass/siteinfo_drop.csv", header=TRUE) #Transpose so its one rows:sample, column:OTU worm_matrix <- t(worm) #labels row.names(worm) <-worm$Sample row.names(worm.env) <-worm.env$Sample #Calculate distance worm.dis <- vegdist(worm_matrix) #View stresses worm.mds0 <-monoMDS(worm.dis) stressplot(worm.mds0, worm.dis) #Make MDS worm.mds <- metaMDS(worm_matrix, trace = FALSE) plot(worm.mds, type = "p") ##t = labeled, p = points fac<-worm.env$Site ## choose factor for grouping #ordispider(worm.mds,group=fac) ##also ordihull OR ordiellipse(worm.mds,group=fac, label=TRUE) #environmental variables ef <- envfit(worm.mds ~ As + Cd + Cu + Fe + pH, worm.env) plot(ef) #Save to pdf #pdf(file='c:/temp/hist.pdf') #plot(x) #dev.off()