*This document details Kegg pathways and creation of the presence/absence plot*

Contigs to push through to the end of my workflow: s11.ctg000012l and s15.ctg000016c.

Get KO annotations and subset for the above contigs

```{r}
# get data
ko <- read.table("../../../Library/CloudStorage/GoogleDrive-jwinter2@uw.edu/Shared drives/Rocap Lab/Project_ODZ_Marinimicrobia_Jordan/Annotations/1058_P1_2018_585_0.2um_assembly_plus_KO_best_only.txt", sep = "\t", header = T)

ko$contig <- paste0(str_split_fixed(ko$gene_callers_id, "_", 3)[,1], "_", str_split_fixed(ko$gene_callers_id, "_", 3)[,2])

# subset data for now
ko <- subset(ko, contig == "MG1058_s11.ctg000012l" | contig == "MG1058_s0.ctg000001c" | contig == "MG1058_s285.ctg000300l" | contig == "MG1058_s526.ctg000549c" | contig == "MG1058_s15.ctg000016c" | contig == "MG1058_s273.ctg000288c" | contig == "MG1058_s408.ctg000428c")

sulf11 <- which(ko$contig == "MG1058_s11.ctg000012l" | ko$contig == "MG1058_s0.ctg000001c" | ko$contig == "MG1058_s285.ctg000300l" | ko$contig == "MG1058_s526.ctg000549c")
ko$bin <- "sulf15"
ko$bin[sulf11] <- "sulf11"
```

Annotate contigs with general metabolisms of interest

```{r}
genes <- read.csv("../data/KO_numbers.csv")
colnames(genes) <- c("accession", "pathway")
ko <- merge(ko, genes)

# count how many genes there are of each pathway
all_paths <- unique(genes$pathway)
pathway <- NULL

for (one_contig in unique(ko$contig)){
  ko_small <- subset(ko, contig == one_contig)
  results <- NULL
  for (i in 1:length(all_paths)){
    path <- all_paths[i]
    results$count[i] <- length(which(ko_small$pathway == path))
    results$path[i] <- path
  }
  results <- as.data.frame(results)
  results$bin <- one_contig
  pathway <- rbind(pathway, results)
}

pathway$presence <- "no"
index <- which(pathway$count > 0)
pathway$presence[index] <- "yes"
```

Plot genes of interest

```{r}
# presence-absence
a <- ggplot(pathway, aes(bin, path, fill=presence)) +
  geom_tile(color="black") +
  scale_x_discrete(guide = guide_axis(n.dodge = 2)) +
  scale_fill_grey(start = 1, end = 0.5) +
  theme_bw()
a
```

