illumina_ar_gene_preprocess.rmd

---
title: "AR gene contaminant check"
author: "Chenhao Li"
date: "2/10/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Load generic libraries
```{r message=FALSE, warning=FALSE}
source('configuration.r')
```

Load plot specific libraries
```{r message=FALSE, warning=FALSE}
```

Merge data
```{r}
metadata <-read.table("../metadata/illumina_metadata.txt",sep="\t",head=T) 
anti <-read.table("../tables/illumina_AR_gene_assignment.dat",sep="\t",head=T)
b1lib <- (filter(metadata, timept %in% c(1, 2)) %>% pull(Library))
b2lib <- (filter(metadata, timept %in% c(3)) %>% pull(Library))
batch1 <- filter(anti, Lib %in% b1lib)
batch2 <- filter(anti, Lib %in% b2lib)

b1prev <- filter(batch1, Cover > 0) %>% count(Anti) %>% mutate(n=n/length(unique(b1lib)))
b2prev <- filter(batch2, Cover > 0) %>% count(Anti) %>% mutate(n=n/length(unique(b2lib)))

tmp <- merge(b1prev,  b2prev, by=1, all=TRUE)
tmp[is.na(tmp)] <- 0

ggplot(tmp, aes(x=n.x, y=n.y)) + 
  geom_point() + 
  xlim(0,1) +
  ylim(0,1) + 
  labs(x="Batch 1", y="Batch 2")
  geom_abline(intercept = 0, slope = 1)
```