mrow workflow

Script

# R Script authored by Daniel Pass, Cardiff University, UK
# 3rd December 2013
# 

library(vegan)

#Load data
worm <-read.csv(worm_gen_matrix_drop, header=TRUE)
worm.env <- read.csv(siteinfo_drop, 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
png(stresses)
worm.mds0 <-monoMDS(worm.dis)
stressplot(worm.mds0, worm.dis)
dev.off()


#Make MDS
png(NMDS)
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)
dev.off()

#Save to pdf
#pdf(file='c:/temp/hist.pdf')
#plot(x)
#dev.off()

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