16S SIMPER

```{r SIMPER: Transects}
library("labdsv")
library("vegan")
library("ggplot2")
library("dplyr")
library("tidyverse")
library("tidyr")
library("clustsig")
```

```{r load data}
setwd("~/Dropbox/UTS/PhD/Projects/Chapter2_RoseBay/Data_Analysis/Data/16S/Data")
sample_data <- read_csv('SMD.rarefied.csv')
asv_rarefy30k_long <- read_csv("asv_rarefy30k_long.csv")
```

```{bash}
qsub -I -q c3b -l ncpus=11,mem=375GB,walltime=72:00:00 
qsub -I -l ncpus=11,mem=375GB,walltime=120:00:00
cd /shared/c3/projects/Nathan.Williams.12034652/Rose-Bay/fastq_and_analysis/SIMPER
module load devel/R-current;
```

```{r Arrange Data on HPC}
library("labdsv")
library("vegan")
library("ggplot2")
library("dplyr")
library("tidyverse")
library("tidyr")
library("clustsig")

sample_data <- read_csv('SMD.rarefied.csv')
asv_rarefy30k_long <- read_csv("asv_rarefy30k_long.csv")

Abundance <- asv_rarefy30k_long %>% select(FGID, SampleID, Abundance_Vegan_Rarefied) %>% distinct()
Abundance.spread <- Abundance %>% spread(key='SampleID', value='Abundance_Vegan_Rarefied', fill=0)
rownames(sample_data) <- sample_data$SampleID
rb.matrix.simper <-  as.matrix(Abundance.spread[,-c(1)])
rownames(rb.matrix.simper) <- Abundance.spread$FGID
rb.matrix.simper.t <- t(rb.matrix.simper)
rb.matrix.nz <- rb.matrix.simper.t[,colSums(rb.matrix.simper.t)!=0]
```

```{r Run SIMPER}
simper.weather <- simper(rb.matrix.nz, group = sample_data$Distance_Offshore, permutations = 999);
saveRDS(simper.weather, 'simper.weather.RDS')
```

```{r SIMPER: load in simper data}
setwd("~/Dropbox/UTS/PhD/Projects/Chapter2_RoseBay/Data_Analysis/Data/16S/Data")
simper <- readRDS("simper.weather.RDS")
summary(simper, ordered = TRUE, digits = 3)
```

```{r}
summary(simper, ordered = TRUE, digits = 3)

simper_pretty <- simper.pretty(rb.matrix.nz, sample_data, c('Location'), perc_cutoff=0.5, low_cutoff = '0.01', low_val=0.01, 'sigASVcontrib')
```