Lat_HSP60_SIMPER.Rmd

---
title: "RBW SIMPER"
---

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

```{r Load in Data}
setwd("~/Dropbox/UTS/PhD/Projects/Chapter1_Vibrio_latitude_study/Data/HSP60/Data")
sample_data <- read_csv('SMD.csv')
HSP60_data_long <- read_csv("HSP60_data_long.csv")
```

```{r Filter Data}
sample_data <- sample_data %>% filter(!Location == "Cairns B") %>% filter(!Location == "Cairns R")
HSP60_data_long <- HSP60_data_long %>% filter(!Location == "Cairns B") %>% filter(!Location == "Cairns R")
```

```{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/Vibrio_Latitude_Project/Vibrio_Latitude_16S_Rerun/fastq_and_analysis/SIMPER
module load devel/R-current;
R
```

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

setwd("~/Dropbox/UTS/PhD/Projects/Chapter1_Vibrio_latitude_study/Data/HSP60/Data")
sample_data <- read_csv('SMD_SIMPER.csv')
HSP60_data_long <- read_csv("HSP60_data_long.csv")
sample_data <- sample_data %>% filter(!Location == "Cairns B") %>% filter(!Location == "Cairns R")
HSP60_data_long <- HSP60_data_long %>% filter(!Location == "Cairns B") %>% filter(!Location == "Cairns R")
```

```{r Arrange}
Abundance <- HSP60_data_long %>% select(GS, SampleID, RA) %>% distinct()
Abundance.spread <- Abundance %>% spread(key='SampleID', value='RA', fill=0)
rownames(sample_data) <- sample_data$SampleID
L.matrix.simper <-  as.matrix(Abundance.spread[,-c(1)])
rownames(L.matrix.simper) <- Abundance.spread$GS
L.matrix.simper.t <- t(L.matrix.simper)
L.matrix.nz <- L.matrix.simper.t[,colSums(L.matrix.simper.t)!=0]
```

```{r Run SIMPER}
simper.L <- simper(L.matrix.nz, group = sample_data$Koppen_classification, permutations = 999);
setwd("~/Dropbox/UTS/PhD/Projects/Chapter1_Vibrio_latitude_study/Data/HSP60/Statistics_Output")
saveRDS(simper.L, 'simper.L.RDS')
```

```{r SIMPER: load in simper data}
setwd("~/Dropbox/UTS/PhD/Projects/Chapter1_Vibrio_latitude_study/Data/HSP60/Statistics_Output")
simper <- readRDS("simper.L.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')
```

```{r}
simper.pretty = function(x, metrics, interesting, perc_cutoff, low_cutoff, low_val, output_name){
  library(vegan)
  #handling otu tables for taxa levels
  save=list(0)
  if(grepl("Otu", colnames(x)[1])!=TRUE){
    #converts output from A.Neumann Taxonomy script
    save=list(58)
    x=as.data.frame(t(x))
    orig_names=colnames(x)
    new_names=list()
    l=1
    for(n in colnames(x)){
      ifelse((l<10), (colnames(x)[l]=c(paste0('Otu000',c(l)))), (colnames(x)[l]=c(paste0('Otu00',c(l))))) 
      new_names=append(new_names, colnames(x)[l])
      l=l+1
    }
    orig_names=as.data.frame(orig_names, row.names = as.character(new_names))
  }
  #running simper
  for(variables in interesting){
    test_1=with(metrics, simper(x, metrics[[variables]]))
    #parsing through simper output, saving desired info to table
    for(name in names(test_1)){
      testmx=matrix(ncol=length(interesting))
      testmx=cbind(test_1[[name]]$ord,test_1[[name]]$cusum)
      sorted=testmx[order(testmx[,1]),]
      sorted=cbind(sorted,test_1[[name]]$species)
      sorted=sorted[order(sorted[,2]),]
      t=matrix(sorted[sorted[,2]<=perc_cutoff,],ncol=3)
      i=nrow(t)
      #converting percents to percent of whole
      while(i>1){
        t[i,2]=as.character(as.numeric(t[i,2])-as.numeric(t[i-1,2]))
        i=i-1
      }
      t[,1]=name
      write.table(t,file=paste(output_name,'_simper.csv',sep=""), append=TRUE, sep=",", col.names = FALSE)
    }}
  y=read.table(paste(output_name,'_simper.csv',sep=""), header=FALSE,sep=",",fill = TRUE,row.names = NULL)
  file.remove(paste(output_name,'_simper.csv',sep = ""))
  y=y[-c(1)]
  colnames(y) = c("Comparison", "SIMPER", "OTU")
  #removing results lower than low cutoff
  if(low_cutoff=='y'){
    y=y[!(as.numeric(as.character(y$SIMPER))<low_val),]
  }
  #prevents changing of colnames if OTU table
  if(58 %in% save){
    y$OTU=orig_names[match(y$OTU, rownames(orig_names)),1]
  }
  write.csv(y,file=paste(output_name,'_clean_simper.csv', sep=''))
}

```