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# Cassandra Wattenburger
# 01/24/18
# Cleaned up scripts to generate beta diversity data and figs 2 and 4
############################################
library("phyloseq")
library("vegan")
library("ggplot2")
library("plyr")
library("ggplot2")
library("tidyr")
library("reshape2")
library("cowplot")
setwd("Y:/Cassi/Sequencing Data/Argonne 2017/01 DEV Project/03 Final Scripts and figures")
#########
#16s Data
rm(list=ls())
###################
#Create ordinations
#load phyloseq object with normalized and pre-processed count data
load("DEV16S.physeq.want.RData")
physeq.want
############################################################################################################################
load("DEV16S.ord.nmds.RData")
############################################################################################################################
#calculate distance using Bray-Curtis method
dist <- distance(physeq.want, method="bray")
#PCoA ordination
ord.pcoa <- ordinate(physeq.want, "PCoA", distance=dist)
#graph PCoA
ord.pcoa.plot <- plot_ordination(physeq.want, ord.pcoa, color = "Compartment", shape = "Soil") +
facet_wrap(~Timepoint) +
ggtitle("16S PCoA using Bray-Curtis Dissimilarity") +
stat_ellipse(type="t")
ord.pcoa.plot
#NMDS ordination
set.seed(2)
ord.nmds <- ordinate(physeq.want, "NMDS", distance=dist)
ord.nmds
#graph NMDS
ord.nmds.plot <- plot_ordination(physeq.want, ord.nmds, color = "Compartment", shape = "Soil") +
facet_wrap(~Timepoint) +
ggtitle("16S NMDS using Bray-Curtis Dissimilarity") +
stat_ellipse(type="t")
ord.nmds.plot
#stress = 0.142
#PCoA and NMDS give similar ordinations
#I'll stick with NMDS because it's non-euclidean
###########
#Statistics
#make a dataframe to run PErMANOVA on
adonis.df = as(sample_data(physeq.want), "data.frame")
#Full model without block effect, since it is a random effect
#constrained to block
set.seed(2)
full <- adonis(dist~Soil*Compartment*Timepoint, data = adonis.df, strata=adonis.df$Block, permutations = 9999)
full
# Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#Soil 1 1.6901 1.6901 24.248 0.06457 0.0001 ***
#Compartment 2 7.2639 3.6320 52.108 0.27753 0.0001 ***
#Timepoint 3 1.4585 0.4862 6.975 0.05573 0.0001 ***
#Soil:Compartment 2 0.3913 0.1957 2.807 0.01495 0.0011 **
#Soil:Timepoint 3 0.2740 0.0913 1.310 0.01047 0.0943 .
#Compartment:Timepoint 6 1.5458 0.2576 3.696 0.05906 0.0001 ***
#Soil:Compartment:Timepoint 6 0.3767 0.0628 0.901 0.01439 0.5692
#Residuals 189 13.1734 0.0697 0.50330
#Total 212 26.1738 1.00000
#another full model to see if significance changes
set.seed(2)
full2 <- adonis(dist~Compartment*Soil*Timepoint, data = adonis.df, strata=adonis.df$Block, permutations = 9999)
full2
#no change in significance
#Mixed model to investigate block effect
#Block is a random effect so exclude from interactions
set.seed(2)
mixed <- adonis(dist~Soil*Compartment*Timepoint+Block, data = adonis.df, strata=adonis.df$Block, permutations = 9999)
mixed
#Call:
#adonis(formula = dist ~ Soil * Compartment * Timepoint + Block, data = adonis.df, permutations = 9999, strata = adonis.df$Block)
#Blocks: strata
#Permutation: free
#Number of permutations: 9999
#Terms added sequentially (first to last)
#Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#Soil 1 1.6901 1.6901 26.530 0.06457 0.0001 ***
#Compartment 2 7.2639 3.6320 57.012 0.27753 0.0001 ***
#Timepoint 3 1.4585 0.4862 7.632 0.05573 0.0001 ***
#Block 2 1.2601 0.6300 9.890 0.04814 0.0001 ***
#Soil:Compartment 2 0.3930 0.1965 3.084 0.01501 0.0009 ***
#Soil:Timepoint 3 0.2746 0.0915 1.437 0.01049 0.0714 .
#Compartment:Timepoint 6 1.5450 0.2575 4.042 0.05903 0.0001 ***
#Soil:Compartment:Timepoint 6 0.3758 0.0626 0.983 0.01436 0.4732
#Residuals 187 11.9128 0.0637 0.45514
#Total 212 26.1738 1.00000
#graph to try to see interaction of comp*time
ord.nmds.plot2 <- plot_ordination(physeq.want, ord.nmds, color = "Timepoint") +
facet_grid(Soil~Compartment) +
ggtitle("16S NMDS using Bray-Curtis Dissimilarity") +
stat_ellipse(type="t")
ord.nmds.plot2
#rhizoplane seems to change across time differently than bulk and rhizosphere
##########
#Contrasts
#To pick apart significance between communities of interest
#Will use PERMANOVA with Bonferroni correction for multiple testing
#create data frame
#OTU data
otu = as(otu_table(physeq.want), "matrix")
head(otu[,1:5])
otu.trans <- t(otu)
head(otu.trans[,1:5])
dim(otu.trans)
#meta data
meta <- sample_data(physeq.want)
head(meta)
dim(meta)
#Merge otu and metadata
otu.meta <- merge(meta, otu.trans, by=0)
head(otu.meta[,1:10])
dim(otu.meta)
rownames(otu.meta) <- otu.meta[,1]
head(otu.meta[,1:10])
otu.meta <- otu.meta[,-1]
head(otu.meta[,1:10])
#################################################
#Bulk vs rhizosphere for each time point and soil
#TP1 Conv.
head(otu.meta[,1:10])
tp1.conv.brs <- subset(otu.meta, Timepoint=="TP1")
tp1.conv.brs <- subset(tp1.conv.brs, Soil=="Conv.")
tp1.conv.brs <- tp1.conv.brs[!(tp1.conv.brs$Compartment=="rhizoplane"),]
head(tp1.conv.brs[,1:10])
dim(tp1.conv.brs)
dist.tp1.conv.brs <- vegdist(tp1.conv.brs[,-(1:5)], method="bray")
set.seed(3)
test1 <- adonis(dist.tp1.conv.brs~Compartment, data=tp1.conv.brs, strata=tp1.conv.brs$Block, permutation=9999)
tp1.conv.brs.p <- test1$aov.tab$`Pr(>F)`[1]
tp1.conv.brs.p
#P=0.0058
#TP1 Div.
tp1.div.brs <- subset(otu.meta, Timepoint=="TP1")
tp1.div.brs <- subset(tp1.div.brs, Soil=="Div.")
tp1.div.brs <- tp1.div.brs[!(tp1.div.brs$Compartment=="rhizoplane"),]
head(tp1.div.brs[,1:10])
dim(tp1.div.brs)
dist.tp1.div.brs <- vegdist(tp1.div.brs[,-(1:5)], method="bray")
set.seed(3)
test2 <- adonis(dist.tp1.div.brs~Compartment, data=tp1.div.brs, strata=tp1.div.brs$Block, permutation=9999)
tp1.div.brs.p <- test2$aov.tab$`Pr(>F)`[1]
tp1.div.brs.p
#P=0.0551
#TP2 Conv.
tp2.conv.brs <- subset(otu.meta, Timepoint=="TP2")
tp2.conv.brs <- subset(tp2.conv.brs, Soil=="Conv.")
tp2.conv.brs <- tp2.conv.brs[!(tp2.conv.brs$Compartment=="rhizoplane"),]
head(tp2.conv.brs[,1:10])
dim(tp2.conv.brs)
dist.tp2.conv.brs <- vegdist(tp2.conv.brs[,-(1:5)], method="bray")
set.seed(3)
test3 <- adonis(dist.tp2.conv.brs~Compartment, data=tp2.conv.brs, strata=tp2.conv.brs$Block, permutation=9999)
tp2.conv.brs.p <- test3$aov.tab$`Pr(>F)`[1]
tp2.conv.brs.p
#P=0.0007
#TP2 Div.
tp2.div.brs <- subset(otu.meta, Timepoint=="TP2")
tp2.div.brs <- subset(tp2.div.brs, Soil=="Div.")
tp2.div.brs <- tp2.div.brs[!(tp2.div.brs$Compartment=="rhizoplane"),]
head(tp2.div.brs[,1:10])
dim(tp2.div.brs)
dist.tp2.div.brs <- vegdist(tp2.div.brs[,-(1:5)], method="bray")
set.seed(3)
test4 <- adonis(dist.tp2.div.brs~Compartment, data=tp2.div.brs, strata=tp2.div.brs$Block, permutation=9999)
tp2.div.brs.p <- test4$aov.tab$`Pr(>F)`[1]
tp2.div.brs.p
#P=0.0086
#TP3 Conv.
head(otu.meta[,1:10])
tp3.conv.brs <- subset(otu.meta, Timepoint=="TP3")
tp3.conv.brs <- subset(tp3.conv.brs, Soil=="Conv.")
tp3.conv.brs <- tp3.conv.brs[!(tp3.conv.brs$Compartment=="rhizoplane"),]
head(tp3.conv.brs[,1:10])
dim(tp3.conv.brs)
dist.tp3.conv.brs <- vegdist(tp3.conv.brs[,-(1:5)], method="bray")
set.seed(3)
test5 <- adonis(dist.tp3.conv.brs~Compartment, data=tp3.conv.brs, strata=tp3.conv.brs$Block, permutation=9999)
tp3.conv.brs.p <- test5$aov.tab$`Pr(>F)`[1]
tp3.conv.brs.p
#P=0.0002
#TP3 Div.
tp3.div.brs <- subset(otu.meta, Timepoint=="TP3")
tp3.div.brs <- subset(tp3.div.brs, Soil=="Div.")
tp3.div.brs <- tp3.div.brs[!(tp3.div.brs$Compartment=="rhizoplane"),]
head(tp3.div.brs[,1:10])
dim(tp3.div.brs)
dist.tp3.div.brs <- vegdist(tp3.div.brs[,-(1:5)], method="bray")
set.seed(3)
test6 <- adonis(dist.tp3.div.brs~Compartment, data=tp3.div.brs, strata=tp3.div.brs$Block, permutation=9999)
tp3.div.brs.p <- test6$aov.tab$`Pr(>F)`[1]
tp3.div.brs.p
#P=0.1463
#TP4 Conv.
head(otu.meta[,1:10])
tp4.conv.brs <- subset(otu.meta, Timepoint=="TP4")
tp4.conv.brs <- subset(tp4.conv.brs, Soil=="Conv.")
tp4.conv.brs <- tp4.conv.brs[!(tp4.conv.brs$Compartment=="rhizoplane"),]
head(tp4.conv.brs[,1:10])
dim(tp4.conv.brs)
dist.tp4.conv.brs <- vegdist(tp4.conv.brs[,-(1:5)], method="bray")
set.seed(3)
test7 <- adonis(dist.tp4.conv.brs~Compartment, data=tp4.conv.brs, strata=tp4.conv.brs$Block, permutation=9999)
tp4.conv.brs.p <- test7$aov.tab$`Pr(>F)`[1]
tp4.conv.brs.p
#P=0.0037
#TP4 Div.
tp4.div.brs <- subset(otu.meta, Timepoint=="TP4")
tp4.div.brs <- subset(tp4.div.brs, Soil=="Div.")
tp4.div.brs <- tp4.div.brs[!(tp4.div.brs$Compartment=="rhizoplane"),]
head(tp4.div.brs[,1:10])
dim(tp4.div.brs)
dist.tp4.div.brs <- vegdist(tp4.div.brs[,-(1:5)], method="bray")
set.seed(3)
test8 <- adonis(dist.tp4.div.brs~Compartment, data=tp4.div.brs, strata=tp4.div.brs$Block, permutation=9999)
tp4.div.brs.p <- test8$aov.tab$`Pr(>F)`[1]
tp4.div.brs.p
#P=0.0504
#Adjust for multiple comparisons
#54 is the total number of contrasts done in this script
p.adj1 <- p.adjust(c(tp1.conv.brs.p, tp1.div.brs.p, tp2.conv.brs.p, tp2.div.brs.p,
tp3.conv.brs.p, tp3.div.brs.p, tp4.conv.brs.p, tp4.div.brs.p), method="bonferroni", n=54)
p.adj1
###############################################
#Bulk vs rhizoplane for each timepoint and soil
#TP1 Conv.
head(otu.meta[,1:10])
tp1.conv.brp <- subset(otu.meta, Timepoint=="TP1")
tp1.conv.brp <- subset(tp1.conv.brp, Soil=="Conv.")
tp1.conv.brp <- tp1.conv.brp[!(tp1.conv.brp$Compartment=="rhizosphere"),]
head(tp1.conv.brp[,1:10])
dim(tp1.conv.brp)
dist.tp1.conv.brp <- vegdist(tp1.conv.brp[,-(1:5)], method="bray")
set.seed(3)
test9 <- adonis(dist.tp1.conv.brp~Compartment, data=tp1.conv.brp, strata=tp1.conv.brp$Block, permutation=9999)
tp1.conv.brp.p <- test9$aov.tab$`Pr(>F)`[1]
tp1.conv.brp.p
#P=0.0004
#TP1 Div.
tp1.div.brp <- subset(otu.meta, Timepoint=="TP1")
tp1.div.brp <- subset(tp1.div.brp, Soil=="Div.")
tp1.div.brp <- tp1.div.brp[!(tp1.div.brp$Compartment=="rhizosphere"),]
head(tp1.div.brp[,1:10])
dim(tp1.div.brp)
dist.tp1.div.brp <- vegdist(tp1.div.brp[,-(1:5)], method="bray")
set.seed(3)
test10 <- adonis(dist.tp1.div.brp~Compartment, data=tp1.div.brp, strata=tp1.div.brp$Block, permutation=9999)
tp1.div.brp.p <- test10$aov.tab$`Pr(>F)`[1]
tp1.div.brp.p
#P=0.0001
#TP2 Conv.
tp2.conv.brp <- subset(otu.meta, Timepoint=="TP2")
tp2.conv.brp <- subset(tp2.conv.brp, Soil=="Conv.")
tp2.conv.brp <- tp2.conv.brp[!(tp2.conv.brp$Compartment=="rhizosphere"),]
head(tp2.conv.brp[,1:10])
dim(tp2.conv.brp)
dist.tp2.conv.brp <- vegdist(tp2.conv.brp[,-(1:5)], method="bray")
set.seed(3)
test11 <- adonis(dist.tp2.conv.brp~Compartment, data=tp2.conv.brp, strata=tp2.conv.brp$Block, permutation=9999)
tp2.conv.brp.p <- test11$aov.tab$`Pr(>F)`[1]
tp2.conv.brp.p
#P=0.0005, significant
#TP2 Div.
tp2.div.brp <- subset(otu.meta, Timepoint=="TP2")
tp2.div.brp <- subset(tp2.div.brp, Soil=="Div.")
tp2.div.brp <- tp2.div.brp[!(tp2.div.brp$Compartment=="rhizosphere"),]
head(tp2.div.brp[,1:10])
dim(tp2.div.brp)
dist.tp2.div.brp <- vegdist(tp2.div.brp[,-(1:5)], method="bray")
set.seed(3)
test12 <- adonis(dist.tp2.div.brp~Compartment, data=tp2.div.brp, strata=tp2.div.brp$Block, permutation=9999)
tp2.div.brp.p <- test12$aov.tab$`Pr(>F)`[1]
tp2.div.brp.p
#P=0.0005
#TP3 Conv.
head(otu.meta[,1:10])
tp3.conv.brp <- subset(otu.meta, Timepoint=="TP3")
tp3.conv.brp <- subset(tp3.conv.brp, Soil=="Conv.")
tp3.conv.brp <- tp3.conv.brp[!(tp3.conv.brp$Compartment=="rhizosphere"),]
head(tp3.conv.brp[,1:10])
dim(tp3.conv.brp)
dist.tp3.conv.brp <- vegdist(tp3.conv.brp[,-(1:5)], method="bray")
set.seed(3)
test13 <- adonis(dist.tp3.conv.brp~Compartment, data=tp3.conv.brp, strata=tp3.conv.brp$Block, permutation=9999)
tp3.conv.brp.p <- test13$aov.tab$`Pr(>F)`[1]
tp3.conv.brp.p
#P=0.0004
#TP3 Div.
tp3.div.brp <- subset(otu.meta, Timepoint=="TP3")
tp3.div.brp <- subset(tp3.div.brp, Soil=="Div.")
tp3.div.brp <- tp3.div.brp[!(tp3.div.brp$Compartment=="rhizosphere"),]
head(tp3.div.brp[,1:10])
dim(tp3.div.brp)
dist.tp3.div.brp <- vegdist(tp3.div.brp[,-(1:5)], method="bray")
set.seed(3)
test14 <- adonis(dist.tp3.div.brp~Compartment, data=tp3.div.brp, strata=tp3.div.brp$Block, permutation=9999)
tp3.div.brp.p <- test14$aov.tab$`Pr(>F)`[1]
tp3.div.brp.p
#P=0.0005
#TP4 Conv.
head(otu.meta[,1:10])
tp4.conv.brp <- subset(otu.meta, Timepoint=="TP4")
tp4.conv.brp <- subset(tp4.conv.brp, Soil=="Conv.")
tp4.conv.brp <- tp4.conv.brp[!(tp4.conv.brp$Compartment=="rhizosphere"),]
head(tp4.conv.brp[,1:10])
dim(tp4.conv.brp)
dist.tp4.conv.brp <- vegdist(tp4.conv.brp[,-(1:5)], method="bray")
set.seed(3)
test15 <- adonis(dist.tp4.conv.brp~Compartment, data=tp4.conv.brp, strata=tp4.conv.brp$Block, permutation=9999)
tp4.conv.brp.p <- test15$aov.tab$`Pr(>F)`[1]
tp4.conv.brp.p
#P=0.0005
#TP4 Div.
tp4.div.brp <- subset(otu.meta, Timepoint=="TP4")
tp4.div.brp <- subset(tp4.div.brp, Soil=="Div.")
tp4.div.brp <- tp4.div.brp[!(tp4.div.brp$Compartment=="rhizosphere"),]
head(tp4.div.brp[,1:10])
dim(tp4.div.brp)
dist.tp4.div.brp <- vegdist(tp4.div.brp[,-(1:5)], method="bray")
set.seed(3)
test16 <- adonis(dist.tp4.div.brp~Compartment, data=tp4.div.brp, strata=tp4.div.brp$Block, permutation=9999)
tp4.div.brp.p <- test16$aov.tab$`Pr(>F)`[1]
tp4.div.brp.p
#P=0.001
#Adjust p-values for multiple comparisons
p.adj2 <- p.adjust(c(tp1.conv.brp.p, tp1.div.brp.p, tp2.conv.brp.p, tp2.div.brp.p,
tp3.conv.brp.p, tp3.div.brp.p, tp4.conv.brp.p, tp4.div.brp.p), method="bonferroni", n=54)
p.adj2
#all signficant
###############################
#Bulk vs bulk for each timepoint
#TP1
tp1.b <- subset(otu.meta, Timepoint=="TP1")
tp1.b <- subset(tp1.b, Compartment=="bulk")
head(tp1.b[,1:5])
dim(tp1.b)
dist.tp1.b <- vegdist(tp1.b[,-(1:5)], method="bray")
set.seed(3)
test17 <- adonis(dist.tp1.b~Soil, data=tp1.b, strata=tp1.b$Block, permutation=9999)
tp1.b.p <- test17$aov.tab$`Pr(>F)`[1]
tp1.b.p
#P=0.0005
#TP2
tp2.b <- subset(otu.meta, Timepoint=="TP2")
tp2.b <- subset(tp2.b, Compartment=="bulk")
head(tp2.b[,1:5])
dim(tp2.b)
dist.tp2.b <- vegdist(tp2.b[,-(1:5)], method="bray")
set.seed(3)
test18 <- adonis(dist.tp2.b~Soil, data=tp2.b, strata=tp2.b$Block, permutation=9999)
tp2.b.p <- test18$aov.tab$`Pr(>F)`[1]
tp2.b.p
#P=0.0005
#TP3
tp3.b <- subset(otu.meta, Timepoint=="TP3")
tp3.b <- subset(tp3.b, Compartment=="bulk")
head(tp3.b[,1:5])
dim(tp3.b)
dist.tp3.b <- vegdist(tp3.b[,-(1:5)], method="bray")
set.seed(3)
test19 <- adonis(dist.tp3.b~Soil, data=tp3.b, strata=tp3.b$Block, permutation=9999)
tp3.b.p <- test19$aov.tab$`Pr(>F)`[1]
tp3.b.p
#P=0.0009
#TP4
tp4.b <- subset(otu.meta, Timepoint=="TP4")
tp4.b <- subset(tp4.b, Compartment=="bulk")
head(tp4.b[,1:5])
dim(tp4.b)
dist.tp4.b <- vegdist(tp4.b[,-(1:5)], method="bray")
set.seed(3)
test20 <- adonis(dist.tp4.b~Soil, data=tp4.b, strata=tp4.b$Block, permutation=9999)
tp4.b.p <- test20$aov.tab$`Pr(>F)`[1]
tp4.b.p
#P=0.0005
#Mulitple comparisons p adjustment
p.adj3 <- p.adjust(c(tp1.b.p, tp2.b.p, tp3.b.p, tp4.b.p), method="bonferroni", n=54)
p.adj3
#all significant
############################################
#Rhizosphere vs rhizosphere at each timepoint
#TP1
tp1.rs <- subset(otu.meta, Timepoint=="TP1")
tp1.rs <- subset(tp1.rs, Compartment=="rhizosphere")
head(tp1.rs[,1:5])
dim(tp1.rs)
dist.tp1.rs <- vegdist(tp1.rs[,-(1:5)], method="bray")
set.seed(3)
test21 <- adonis(dist.tp1.rs~Soil, data=tp1.rs, strata=tp1.rs$Block, permutation=9999)
tp1.rs.p <- test21$aov.tab$`Pr(>F)`[1]
tp1.rs.p
#P=0.0005
#TP2
tp2.rs <- subset(otu.meta, Timepoint=="TP2")
tp2.rs <- subset(tp2.rs, Compartment=="rhizosphere")
head(tp2.rs[,1:5])
dim(tp2.rs)
dist.tp2.rs <- vegdist(tp2.rs[,-(1:5)], method="bray")
set.seed(3)
test22 <- adonis(dist.tp2.rs~Soil, data=tp2.rs, strata=tp2.rs$Block, permutation=9999)
tp2.rs.p <- test22$aov.tab$`Pr(>F)`[1]
tp2.rs.p
#P=0.0005
#TP3
tp3.rs <- subset(otu.meta, Timepoint=="TP3")
tp3.rs <- subset(tp3.rs, Compartment=="rhizosphere")
head(tp3.rs[,1:5])
dim(tp3.rs)
dist.tp3.rs <- vegdist(tp3.rs[,-(1:5)], method="bray")
set.seed(3)
test23 <- adonis(dist.tp3.rs~Soil, data=tp3.rs, strata=tp3.rs$Block, permutation=9999)
tp3.rs.p <- test23$aov.tab$`Pr(>F)`[1]
tp3.rs.p
#P=0.0009
#TP4
tp4.rs <- subset(otu.meta, Timepoint=="TP4")
tp4.rs <- subset(tp4.rs, Compartment=="rhizosphere")
head(tp4.rs[,1:5])
dim(tp4.rs)
set.seed(3)
dist.tp4.rs <- vegdist(tp4.rs[,-(1:5)], method="bray")
test24 <- adonis(dist.tp4.rs~Soil, data=tp4.rs, strata=tp4.rs$Block, permutation=9999)
tp4.rs.p <- test24$aov.tab$`Pr(>F)`[1]
tp4.rs.p
#P=0.0005, significant
#Multiple comparisons p-adjustment
p.adj4 <- p.adjust(c(tp1.rs.p, tp2.rs.p, tp3.rs.p, tp4.rs.p), method="bonferroni", n=54)
p.adj4
#all significant
############################################
#Rhizoplane vs rhizoplane at each timepoint
#TP1
tp1.rp <- subset(otu.meta, Timepoint=="TP1")
tp1.rp <- subset(tp1.rp, Compartment=="rhizoplane")
head(tp1.rp[,1:5])
dim(tp1.rp)
dist.tp1.rp <- vegdist(tp1.rp[,-(1:5)], method="bray")
set.seed(3)
test25 <- adonis(dist.tp1.rp~Soil, data=tp1.rp, strata=tp1.rp$Block, permutation=9999)
tp1.rp.p <- test25$aov.tab$`Pr(>F)`[1]
tp1.rp.p
#P=0.0001
#TP2
tp2.rp <- subset(otu.meta, Timepoint=="TP2")
tp2.rp <- subset(tp2.rp, Compartment=="rhizoplane")
head(tp2.rp[,1:5])
dim(tp2.rp)
dist.tp2.rp <- vegdist(tp2.rp[,-(1:5)], method="bray")
set.seed(3)
test26 <- adonis(dist.tp2.rp~Soil, data=tp2.rp, strata=tp2.rp$Block, permutation=9999)
tp2.rp.p <- test26$aov.tab$`Pr(>F)`[1]
tp2.rp.p
#P=0.0005
#TP3
tp3.rp <- subset(otu.meta, Timepoint=="TP3")
tp3.rp <- subset(tp3.rp, Compartment=="rhizoplane")
head(tp3.rp[,1:5])
dim(tp3.rp)
dist.tp3.rp <- vegdist(tp3.rp[,-(1:5)], method="bray")
set.seed(3)
test27 <- adonis(dist.tp3.rp~Soil, data=tp3.rp, strata=tp3.rp$Block, permutation=9999)
tp3.rp.p <- test27$aov.tab$'Pr(>F)'[1]
tp3.rp.p
#P=0.0011
#TP4
tp4.rp <- subset(otu.meta, Timepoint=="TP4")
tp4.rp <- subset(tp4.rp, Compartment=="rhizoplane")
head(tp4.rp[,1:5])
dim(tp4.rp)
dist.tp4.rp <- vegdist(tp4.rp[,-(1:5)], method="bray")
set.seed(3)
test28 <- adonis(dist.tp4.rp~Soil, data=tp4.rp, strata=tp4.rp$Block, permutation=9999)
tp4.rp.p <- test28$aov.tab$'Pr(>F)'[1]
tp4.rp.p
#P=0.0030
#Multiple comparisons p-adjustment
p.adj5 <- p.adjust(c(tp1.rp.p, tp2.rp.p, tp3.rp.p, tp4.rp.p), method="bonferroni", n=54)
p.adj5
#TP1 and TP2 significant, TP3 and TP4 not
#Explore CompxTime interaction because it's the most biologically significant interaction with visual support in ordinations
##########
#Bulk soil
#TP1 vs TP2 Conv.
conv.b.tp12 <- subset(otu.meta, Compartment=="bulk")
conv.b.tp12 <- subset(conv.b.tp12, Soil=="Conv.")
conv.b.tp12 <- conv.b.tp12[!(conv.b.tp12$Timepoint=="TP3"),]
conv.b.tp12 <- conv.b.tp12[!(conv.b.tp12$Timepoint=="TP4"),]
head(conv.b.tp12[,1:10])
dist.conv.b.tp12 <- vegdist(conv.b.tp12[,-(1:5)], method="bray")
set.seed(3)
test29 <- adonis(dist.conv.b.tp12~Timepoint, data=conv.b.tp12, strata=conv.b.tp12$Block, permutation=9999)
conv.b.tp12.p <- test29$aov.tab$'Pr(>F)'[1]
conv.b.tp12.p
#P=0.003
#TP1 vs TP2 Div.
div.b.tp12 <- subset(otu.meta, Compartment=="bulk")
div.b.tp12 <- subset(div.b.tp12, Soil=="Div.")
div.b.tp12 <- div.b.tp12[!(div.b.tp12$Timepoint=="TP3"),]
div.b.tp12 <- div.b.tp12[!(div.b.tp12$Timepoint=="TP4"),]
head(div.b.tp12[,1:10])
dist.div.b.tp12 <- vegdist(div.b.tp12[,-(1:5)], method="bray")
set.seed(3)
test30 <- adonis(dist.div.b.tp12~Timepoint, data=div.b.tp12, strata=div.b.tp12$Block, permutation=9999)
div.b.tp12.p <- test30$aov.tab$'Pr(>F)'[1]
div.b.tp12.p
#0.1492
#TP2 vs TP3 Conv.
conv.b.tp23 <- subset(otu.meta, Compartment=="bulk")
conv.b.tp23 <- subset(conv.b.tp23, Soil=="Conv.")
conv.b.tp23 <- conv.b.tp23[!(conv.b.tp23$Timepoint=="TP1"),]
conv.b.tp23 <- conv.b.tp23[!(conv.b.tp23$Timepoint=="TP4"),]
head(conv.b.tp23[,1:10])
dist.conv.b.tp23 <- vegdist(conv.b.tp23[,-(1:5)], method="bray")
set.seed(3)
test31 <- adonis(dist.conv.b.tp23~Timepoint, data=conv.b.tp23, strata=conv.b.tp23$Block, permutation=9999)
conv.b.tp23.p <- test31$aov.tab$'Pr(>F)'[1]
conv.b.tp23.p
#P=0.0153
#TP2 vs TP3 Div.
div.b.tp23 <- subset(otu.meta, Compartment=="bulk")
div.b.tp23 <- subset(div.b.tp23, Soil=="Div.")
div.b.tp23 <- div.b.tp23[!(div.b.tp23$Timepoint=="TP1"),]
div.b.tp23 <- div.b.tp23[!(div.b.tp23$Timepoint=="TP4"),]
head(div.b.tp23[,1:10])
dist.div.b.tp23 <- vegdist(div.b.tp23[,-(1:5)], method="bray")
set.seed(3)
test32 <- adonis(dist.div.b.tp23~Timepoint, data=div.b.tp23, strata=div.b.tp23$Block, permutation=9999)
div.b.tp23.p <- test32$aov.tab$'Pr(>F)'[1]
div.b.tp23.p
#P=0.6171
#TP3 vs TP4 Conv.
conv.b.tp34 <- subset(otu.meta, Compartment=="bulk")
conv.b.tp34 <- subset(conv.b.tp34, Soil=="Conv.")
conv.b.tp34 <- conv.b.tp34[!(conv.b.tp34$Timepoint=="TP1"),]
conv.b.tp34 <- conv.b.tp34[!(conv.b.tp34$Timepoint=="TP2"),]
head(conv.b.tp34[,1:10])
dist.conv.b.tp34 <- vegdist(conv.b.tp34[,-(1:5)], method="bray")
set.seed(3)
test33 <- adonis(dist.conv.b.tp34~Timepoint, data=conv.b.tp34, strata=conv.b.tp34$Block, permutation=9999)
conv.b.tp34.p <- test33$aov.tab$'Pr(>F)'[1]
conv.b.tp34.p
#0.1566
#TP3 vs TP4 Div.
div.b.tp34 <- subset(otu.meta, Compartment=="bulk")
div.b.tp34 <- subset(div.b.tp34, Soil=="Div.")
div.b.tp34 <- div.b.tp34[!(div.b.tp34$Timepoint=="TP1"),]
div.b.tp34 <- div.b.tp34[!(div.b.tp34$Timepoint=="TP2"),]
head(div.b.tp34[,1:10])
dist.div.b.tp34 <- vegdist(div.b.tp34[,-(1:5)], method="bray")
set.seed(3)
test34 <- adonis(dist.div.b.tp34~Timepoint, data=div.b.tp34, strata=div.b.tp34$Block, permutation=9999)
div.b.tp34.p <- test34$aov.tab$'Pr(>F)'[1]
div.b.tp34.p
#0.6474
#Multiple comparisons p adjustment
padj6 <- p.adjust(c(conv.b.tp12.p, div.b.tp12.p, conv.b.tp23.p, div.b.tp23.p, conv.b.tp34.p, div.b.tp34.p),
method="bonferroni", n=54)
padj6
#no significance
#################
#Rhizosphere soil
#TP1 vs TP2 Conv.
conv.rs.tp12 <- subset(otu.meta, Compartment=="rhizosphere")
conv.rs.tp12 <- subset(conv.rs.tp12, Soil=="Conv.")
conv.rs.tp12 <- conv.rs.tp12[!(conv.rs.tp12$Timepoint=="TP3"),]
conv.rs.tp12 <- conv.rs.tp12[!(conv.rs.tp12$Timepoint=="TP4"),]
head(conv.rs.tp12[,1:10])
dist.conv.rs.tp12 <- vegdist(conv.rs.tp12[,-(1:5)], method="bray")
set.seed(3)
test35 <- adonis(dist.conv.rs.tp12~Timepoint, data=conv.rs.tp12, strata=conv.rs.tp12$Block, permutation=9999)
conv.rs.tp12.p <- test35$aov.tab$'Pr(>F)'[1]
conv.rs.tp12.p
#0.0021
#TP1 vs TP2 Div.
div.rs.tp12 <- subset(otu.meta, Compartment=="rhizosphere")
div.rs.tp12 <- subset(div.rs.tp12, Soil=="Div.")
div.rs.tp12 <- div.rs.tp12[!(div.rs.tp12$Timepoint=="TP3"),]
div.rs.tp12 <- div.rs.tp12[!(div.rs.tp12$Timepoint=="TP4"),]
head(div.rs.tp12[,1:10])
dist.div.rs.tp12 <- vegdist(div.rs.tp12[,-(1:5)], method="bray")
set.seed(3)
test36 <- adonis(dist.div.rs.tp12~Timepoint, data=div.rs.tp12, strata=div.rs.tp12$Block, permutation=9999)
div.rs.tp12.p <- test36$aov.tab$'Pr(>F)'[1]
div.rs.tp12.p
#0.0021
#TP2 vs TP3 Conv.
conv.rs.tp23 <- subset(otu.meta, Compartment=="rhizosphere")
conv.rs.tp23 <- subset(conv.rs.tp23, Soil=="Conv.")
conv.rs.tp23 <- conv.rs.tp23[!(conv.rs.tp23$Timepoint=="TP1"),]
conv.rs.tp23 <- conv.rs.tp23[!(conv.rs.tp23$Timepoint=="TP4"),]
head(conv.rs.tp23[,1:10])
dist.conv.rs.tp23 <- vegdist(conv.rs.tp23[,-(1:5)], method="bray")
set.seed(3)
test37 <- adonis(dist.conv.rs.tp23~Timepoint, data=conv.rs.tp23, strata=conv.rs.tp23$Block, permutation=9999)
conv.rs.tp23.p <- test37$aov.tab$'Pr(>F)'[1]
conv.rs.tp23.p
#0.0092
#TP2 vs TP3 Div.
div.rs.tp23 <- subset(otu.meta, Compartment=="rhizosphere")
div.rs.tp23 <- subset(div.rs.tp23, Soil=="Div.")
div.rs.tp23 <- div.rs.tp23[!(div.rs.tp23$Timepoint=="TP1"),]
div.rs.tp23 <- div.rs.tp23[!(div.rs.tp23$Timepoint=="TP4"),]
head(div.rs.tp23[,1:10])
dist.div.rs.tp23 <- vegdist(div.rs.tp23[,-(1:5)], method="bray")
set.seed(3)
test38 <- adonis(dist.div.rs.tp23~Timepoint, data=div.rs.tp23, strata=div.rs.tp23$Block, permutation=9999)
div.rs.tp23.p <- test38$aov.tab$'Pr(>F)'[1]
div.rs.tp23.p
#0.0177
#TP3 vs TP4 Conv.
conv.rs.tp34 <- subset(otu.meta, Compartment=="rhizosphere")
conv.rs.tp34 <- subset(conv.rs.tp34, Soil=="Conv.")
conv.rs.tp34 <- conv.rs.tp34[!(conv.rs.tp34$Timepoint=="TP1"),]
conv.rs.tp34 <- conv.rs.tp34[!(conv.rs.tp34$Timepoint=="TP2"),]
head(conv.rs.tp34[,1:10])
dist.conv.rs.tp34 <- vegdist(conv.rs.tp34[,-(1:5)], method="bray")
set.seed(3)
test39 <- adonis(dist.conv.rs.tp34~Timepoint, data=conv.rs.tp34, strata=conv.rs.tp34$Block, permutation=9999)
conv.rs.tp34.p <- test39$aov.tab$'Pr(>F)'[1]
conv.rs.tp34.p
#0.0357
#TP3 vs TP4 Div.
div.rs.tp34 <- subset(otu.meta, Compartment=="rhizosphere")
div.rs.tp34 <- subset(div.rs.tp34, Soil=="Div.")
div.rs.tp34 <- div.rs.tp34[!(div.rs.tp34$Timepoint=="TP1"),]
div.rs.tp34 <- div.rs.tp34[!(div.rs.tp34$Timepoint=="TP2"),]
head(div.rs.tp34[,1:10])
dist.div.rs.tp34 <- vegdist(div.rs.tp34[,-(1:5)], method="bray")
set.seed(3)
test40 <- adonis(dist.div.rs.tp34~Timepoint, data=div.rs.tp34, strata=div.rs.tp34$Block, permutation=9999)
div.rs.tp34.p <- test40$aov.tab$'Pr(>F)'[1]
div.rs.tp34.p
#0.055
#Multiple comparisons p adjustment
p.adj7 <- p.adjust(c(conv.rs.tp12.p, div.rs.tp12.p, conv.rs.tp23.p, div.rs.tp23.p, conv.rs.tp34.p, div.rs.tp34.p),
method="bonferroni", n=54)
p.adj7
#no significance
################
#Rhizoplane soil
#TP1 vs TP2 Conv.
conv.rp.tp12 <- subset(otu.meta, Compartment=="rhizoplane")
conv.rp.tp12 <- subset(conv.rp.tp12, Soil=="Conv.")
conv.rp.tp12 <- conv.rp.tp12[!(conv.rp.tp12$Timepoint=="TP3"),]
conv.rp.tp12 <- conv.rp.tp12[!(conv.rp.tp12$Timepoint=="TP4"),]
head(conv.rp.tp12[,1:10])
dist.conv.rp.tp12 <- vegdist(conv.rp.tp12[,-(1:5)], method="bray")
set.seed(3)
test41 <- adonis(dist.conv.rp.tp12~Timepoint, data=conv.rp.tp12, strata=conv.rp.tp12$Block, permutation=9999)
conv.rp.tp12.p <- test41$aov.tab$'Pr(>F)'[1]
conv.rp.tp12.p
#P=0.0005
#TP1 vs TP2 Div.
div.rp.tp12 <- subset(otu.meta, Compartment=="rhizoplane")
div.rp.tp12 <- subset(div.rp.tp12, Soil=="Div.")
div.rp.tp12 <- div.rp.tp12[!(div.rp.tp12$Timepoint=="TP3"),]
div.rp.tp12 <- div.rp.tp12[!(div.rp.tp12$Timepoint=="TP4"),]
head(div.rp.tp12[,1:10])
dist.div.rp.tp12 <- vegdist(div.rp.tp12[,-(1:5)], method="bray")
set.seed(3)
test42 <- adonis(dist.div.rp.tp12~Timepoint, data=div.rp.tp12, strata=div.rp.tp12$Block, permutation=9999)
div.rp.tp12.p <- test42$aov.tab$'Pr(>F)'[1]
div.rp.tp12.p
#P=0.0004
#TP2 vs TP3 Conv.
conv.rp.tp23 <- subset(otu.meta, Compartment=="rhizoplane")
conv.rp.tp23 <- subset(conv.rp.tp23, Soil=="Conv.")
conv.rp.tp23 <- conv.rp.tp23[!(conv.rp.tp23$Timepoint=="TP1"),]
conv.rp.tp23 <- conv.rp.tp23[!(conv.rp.tp23$Timepoint=="TP4"),]
head(conv.rp.tp23[,1:10])
dist.conv.rp.tp23 <- vegdist(conv.rp.tp23[,-(1:5)], method="bray")
set.seed(3)
test43 <- adonis(dist.conv.rp.tp23~Timepoint, data=conv.rp.tp23, strata=conv.rp.tp23$Block, permutation=9999)
conv.rp.tp23.p <- test43$aov.tab$'Pr(>F)'[1]
conv.rp.tp23.p
#P=0.0004
#TP2 vs TP3 Div.
div.rp.tp23 <- subset(otu.meta, Compartment=="rhizoplane")
div.rp.tp23 <- subset(div.rp.tp23, Soil=="Div.")
div.rp.tp23 <- div.rp.tp23[!(div.rp.tp23$Timepoint=="TP1"),]
div.rp.tp23 <- div.rp.tp23[!(div.rp.tp23$Timepoint=="TP4"),]
head(div.rp.tp23[,1:10])
dist.div.rp.tp23 <- vegdist(div.rp.tp23[,-(1:5)], method="bray")
set.seed(3)
test44 <- adonis(dist.div.rp.tp23~Timepoint, data=div.rp.tp23, strata=div.rp.tp23$Block, permutation=9999)
div.rp.tp23.p <- test44$aov.tab$'Pr(>F)'[1]
div.rp.tp23.p
#P=0.0005
#TP3 vs TP4 Conv.
conv.rp.tp34 <- subset(otu.meta, Compartment=="rhizoplane")
conv.rp.tp34 <- subset(conv.rp.tp34, Soil=="Conv.")
conv.rp.tp34 <- conv.rp.tp34[!(conv.rp.tp34$Timepoint=="TP1"),]
conv.rp.tp34 <- conv.rp.tp34[!(conv.rp.tp34$Timepoint=="TP2"),]
head(conv.rp.tp34[,1:10])
dist.conv.rp.tp34 <- vegdist(conv.rp.tp34[,-(1:5)], method="bray")
set.seed(3)
test45 <- adonis(dist.conv.rp.tp34~Timepoint, data=conv.rp.tp34, strata=conv.rp.tp34$Block, permutation=9999)
conv.rp.tp34.p <- test45$aov.tab$'Pr(>F)'[1]
conv.rp.tp34.p
#P=0.0003
#TP3 vs TP4 Div.
div.rp.tp34 <- subset(otu.meta, Compartment=="rhizoplane")
div.rp.tp34 <- subset(div.rp.tp34, Soil=="Div.")
div.rp.tp34 <- div.rp.tp34[!(div.rp.tp34$Timepoint=="TP1"),]
div.rp.tp34 <- div.rp.tp34[!(div.rp.tp34$Timepoint=="TP2"),]
head(div.rp.tp34[,1:10])
dist.div.rp.tp34 <- vegdist(div.rp.tp34[,-(1:5)], method="bray")
set.seed(3)
test46 <- adonis(dist.div.rp.tp34~Timepoint, data=div.rp.tp34, strata=div.rp.tp34$Block, permutation=9999)
div.rp.tp34.p <- test46$aov.tab$'Pr(>F)'[1]
div.rp.tp34.p
#P=0.0005
#Correct for multiple comparisons
padj8 <- p.adjust(c(conv.rp.tp12.p, div.rp.tp12.p, conv.rp.tp23.p, div.rp.tp23.p, conv.rp.tp34.p, div.rp.tp34.p),
method="bonferroni", n=54)
padj8
#all significant
###################################################
#Rhizosphere vs Rhizoplane for each cropping system
#adding this in after all other comparisons, to make analysis more complete
#TP1 Conv.
head(otu.meta[,1:10])
tp1.conv.rsrp <- subset(otu.meta, Timepoint=="TP1")
tp1.conv.rsrp <- subset(tp1.conv.rsrp, Soil=="Conv.")
tp1.conv.rsrp <- tp1.conv.rsrp[!(tp1.conv.rsrp$Compartment=="bulk"),]
head(tp1.conv.rsrp[,1:10])
dim(tp1.conv.rsrp)
dist.tp1.conv.rsrp <- vegdist(tp1.conv.rsrp[,-(1:5)], method="bray")
set.seed(3)
test47 <- adonis(dist.tp1.conv.rsrp~Compartment, data=tp1.conv.rsrp, strata=tp1.conv.rsrp$Block, permutation=9999)
tp1.conv.rsrp.p <- test47$aov.tab$`Pr(>F)`[1]
tp1.conv.rsrp.p
#P=0.0004
#TP1 Div.
tp1.div.rsrp <- subset(otu.meta, Timepoint=="TP1")
tp1.div.rsrp <- subset(tp1.div.rsrp, Soil=="Div.")
tp1.div.rsrp <- tp1.div.rsrp[!(tp1.div.rsrp$Compartment=="bulk"),]
head(tp1.div.rsrp[,1:10])
dim(tp1.div.rsrp)
dist.tp1.div.rsrp <- vegdist(tp1.div.rsrp[,-(1:5)], method="bray")
set.seed(3)
test48 <- adonis(dist.tp1.div.rsrp~Compartment, data=tp1.div.rsrp, strata=tp1.div.rsrp$Block, permutation=9999)
tp1.div.rsrp.p <- test48$aov.tab$`Pr(>F)`[1]
tp1.div.rsrp.p
#P=0.0001
#TP2 Conv.
tp2.conv.rsrp <- subset(otu.meta, Timepoint=="TP2")
tp2.conv.rsrp <- subset(tp2.conv.rsrp, Soil=="Conv.")
tp2.conv.rsrp <- tp2.conv.rsrp[!(tp2.conv.rsrp$Compartment=="bulk"),]
head(tp2.conv.rsrp[,1:10])
dim(tp2.conv.rsrp)
dist.tp2.conv.rsrp <- vegdist(tp2.conv.rsrp[,-(1:5)], method="bray")
set.seed(3)
test49 <- adonis(dist.tp2.conv.rsrp~Compartment, data=tp2.conv.rsrp, strata=tp2.conv.rsrp$Block, permutation=9999)
tp2.conv.rsrp.p <- test49$aov.tab$`Pr(>F)`[1]
tp2.conv.rsrp.p
#P=0.0005, significant
#TP2 Div.
tp2.div.rsrp <- subset(otu.meta, Timepoint=="TP2")
tp2.div.rsrp <- subset(tp2.div.rsrp, Soil=="Div.")
tp2.div.rsrp <- tp2.div.rsrp[!(tp2.div.rsrp$Compartment=="bulk"),]
head(tp2.div.rsrp[,1:10])
dim(tp2.div.rsrp)
dist.tp2.div.rsrp <- vegdist(tp2.div.rsrp[,-(1:5)], method="bray")
set.seed(3)
test50 <- adonis(dist.tp2.div.rsrp~Compartment, data=tp2.div.rsrp, strata=tp2.div.rsrp$Block, permutation=9999)
tp2.div.rsrp.p <- test50$aov.tab$`Pr(>F)`[1]
tp2.div.rsrp.p
#P=0.0005
#TP3 Conv.
head(otu.meta[,1:10])
tp3.conv.rsrp <- subset(otu.meta, Timepoint=="TP3")
tp3.conv.rsrp <- subset(tp3.conv.rsrp, Soil=="Conv.")
tp3.conv.rsrp <- tp3.conv.rsrp[!(tp3.conv.rsrp$Compartment=="bulk"),]
head(tp3.conv.rsrp[,1:10])
dim(tp3.conv.rsrp)
dist.tp3.conv.rsrp <- vegdist(tp3.conv.rsrp[,-(1:5)], method="bray")
set.seed(3)
test51 <- adonis(dist.tp3.conv.rsrp~Compartment, data=tp3.conv.rsrp, strata=tp3.conv.rsrp$Block, permutation=9999)
tp3.conv.rsrp.p <- test51$aov.tab$`Pr(>F)`[1]
tp3.conv.rsrp.p
#P=0.0004
#TP3 Div.
tp3.div.rsrp <- subset(otu.meta, Timepoint=="TP3")
tp3.div.rsrp <- subset(tp3.div.rsrp, Soil=="Div.")
tp3.div.rsrp <- tp3.div.rsrp[!(tp3.div.rsrp$Compartment=="bulk"),]
head(tp3.div.rsrp[,1:10])
dim(tp3.div.rsrp)
dist.tp3.div.rsrp <- vegdist(tp3.div.rsrp[,-(1:5)], method="bray")
set.seed(3)
test52 <- adonis(dist.tp3.div.rsrp~Compartment, data=tp3.div.rsrp, strata=tp3.div.rsrp$Block, permutation=9999)
tp3.div.rsrp.p <- test52$aov.tab$`Pr(>F)`[1]
tp3.div.rsrp.p
#P=0.0005
#TP4 Conv.
head(otu.meta[,1:10])
tp4.conv.rsrp <- subset(otu.meta, Timepoint=="TP4")
tp4.conv.rsrp <- subset(tp4.conv.rsrp, Soil=="Conv.")
tp4.conv.rsrp <- tp4.conv.rsrp[!(tp4.conv.rsrp$Compartment=="bulk"),]
head(tp4.conv.rsrp[,1:10])
dim(tp4.conv.rsrp)
dist.tp4.conv.rsrp <- vegdist(tp4.conv.rsrp[,-(1:5)], method="bray")
set.seed(3)
test53 <- adonis(dist.tp4.conv.rsrp~Compartment, data=tp4.conv.rsrp, strata=tp4.conv.rsrp$Block, permutation=9999)
tp4.conv.rsrp.p <- test53$aov.tab$`Pr(>F)`[1]
tp4.conv.rsrp.p
#P=0.0005
#TP4 Div.
tp4.div.rsrp <- subset(otu.meta, Timepoint=="TP4")
tp4.div.rsrp <- subset(tp4.div.rsrp, Soil=="Div.")
tp4.div.rsrp <- tp4.div.rsrp[!(tp4.div.rsrp$Compartment=="bulk"),]
head(tp4.div.rsrp[,1:10])
dim(tp4.div.rsrp)
dist.tp4.div.rsrp <- vegdist(tp4.div.rsrp[,-(1:5)], method="bray")
set.seed(3)
test54 <- adonis(dist.tp4.div.rsrp~Compartment, data=tp4.div.rsrp, strata=tp4.div.rsrp$Block, permutation=9999)
tp4.div.rsrp.p <- test54$aov.tab$`Pr(>F)`[1]
tp4.div.rsrp.p
#P=0.001
#Adjust p-values for multiple comparisons
p.adj2 <- p.adjust(c(tp1.conv.rsrp.p, tp1.div.rsrp.p, tp2.conv.rsrp.p, tp2.div.rsrp.p,
tp3.conv.rsrp.p, tp3.div.rsrp.p, tp4.conv.rsrp.p, tp4.div.rsrp.p), method="bonferroni", n=54)
p.adj2
#all signficant