library(knitr)
library(readxl)
#detach(package:plyr)
library(dplyr)
library(ggplot2)
library(reshape2)
library(kableExtra)
library(tidyr)
library(phyloseq)
library(vegan)
library(metagMisc)
set.seed(100)

get files

ss<-read.csv(
  "/Users/kylielanglois/OneDrive - SCCWRP/SD I-O data/biofilm ddPCR/septic sludge/septic sludge processed nodups 060223.csv")

dat<-read.csv("/Users/kylielanglois/OneDrive - SCCWRP/SD I-O data/all SD IO combo 2024/SDIO_fastq_combo_table_norep_nobl_nozero.csv")
dat1<-dat

map<-read.csv("/Users/kylielanglois/OneDrive - SCCWRP/SD I-O data/all SD IO combo 2024/SD_IO_metadata_fastq_combo_012624_norep_nobl_nozero.csv")
map1<-map
rownames(map1)<-map1$SEQUENCING_NAME
map1$SAMPLE_TYPE<-gsub("POT_SEPTIC", "GRABS", map1$SAMPLE_TYPE)

path.for.export<-"/Users/kylielanglois/SCCWRP/KL data - General/project folders/SD_IO/"

sewer vs storm metabarcoding

#anosim: sewer v storm
v.df<-phyloseq_to_df(physeq1, addtax = F, addtot = F) 
#ASV table with only sewers and storm samples

#transform for vegan (samples as rows)
rownames(v.df)<-v.df$OTU
v.df<-v.df[,-1]
v.df.t<-as.data.frame(t(v.df))

a<-anosim(x=v.df.t, 
          grouping = samples_keep$SAMPLE_TYPE, 
          permutations = 999, distance = "bray")
a
## 
## Call:
## anosim(x = v.df.t, grouping = samples_keep$SAMPLE_TYPE, permutations = 999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.4827 
##       Significance: 0.001 
## 
## Permutation: free
## Number of permutations: 999
a1<-anosim(x=v.df.t, 
          grouping = samples_keep$season, 
          permutations = 999, distance = "bray")
a1
## 
## Call:
## anosim(x = v.df.t, grouping = samples_keep$season, permutations = 999,      distance = "bray") 
## Dissimilarity: bray 
## 
## ANOSIM statistic R: 0.4858 
##       Significance: 0.001 
## 
## Permutation: free
## Number of permutations: 999
#permanova: season
p<-adonis2(v.df.t~samples_keep$season, method = "bray")
p
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## adonis2(formula = v.df.t ~ samples_keep$season, method = "bray")
##                      Df SumOfSqs      R2      F Pr(>F)    
## samples_keep$season   1    2.697 0.04182 7.2884  0.001 ***
## Residual            167   61.790 0.95818                  
## Total               168   64.487 1.00000                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

septic sludge ddPCR

Target mean st.dev
ENT 6.61e+08 1.18e+09
HF183 1.12e+07 1.38e+07
Lachno3 1.89e+07 1.65e+07
NP gyrA 2.25e+05 3.95e+05
sketa 4.92e+07 4.78e+07

plot