mrow workflow
Created: 2013-12-03 22:32:46
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Inputs (2)
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Name |
Description |
siteinfo_drop |
|
worm_gen_matrix_drop |
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Processors (1)
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Name |
Type |
Description |
Rshell |
rshell |
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() R Serverlocalhost:6311 |
Beanshells (0)
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Outputs (2)
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Name |
Description |
NMDS |
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stresses |
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Datalinks (4)
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Source |
Sink |
siteinfo_drop |
Rshell:siteinfo_drop |
worm_gen_matrix_drop |
Rshell:worm_gen_matrix_drop |
Rshell:NMDS |
NMDS |
Rshell:stresses |
stresses |
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