Isolate_report_builder.Rmd

---
title: "Ashe Report"
output: pdf_document
params:
  bandage: default
  plasmid: default
  amr: default
  sample: default
  metrics: default
  workDir: default
---

```{r, setup,include=FALSE}
knitr::opts_knit$set(root.dir = params$workDir)
```


```{r load-packages, includes=FALSE, echo=FALSE}
library(knitr)
library(kableExtra)
```

# Sample Metrics
```{r echo=FALSE}
metrics <- read.csv(params$metrics, header = TRUE,sep = "\t")
metrics2 <- subset(metrics, Sample == params$sample)
metrics2 <- t(metrics2)
knitr::kable(metrics2)
```

# AMR Data
```{r echo=FALSE}
data <- read.csv(params$amr,header=TRUE,sep = "\t")
names(data) <- c('prot','contig','start','stop','strand','gene'
   ,'seq','scope','type',
  'subtype','class','subclass','method','targ_len','ref_len',
   'cov','ident','aln_len','acc','closest','hmmID','hmmDes')
data2 <- subset(data, select = -c(prot,scope,type,subtype,subclass,method,
  targ_len,ref_len,cov,ident,aln_len,acc,hmmID,hmmDes,class,closest))
knitr::kable(data2) %>% kable_styling(full_width = T)
```

# Bandage Plot
```{r echo = FALSE, error = FALSE, out.width="50%", fig.align="center"}
temp <- params$bandage
options(knitr.graphics.error = FALSE)
knitr::include_graphics(temp)
```

# Plasmid Data
```{r echo=FALSE, out.width="150%", eval = FALSE}
plas <- read.csv(params$plasmid,header = TRUE,sep = "\t")
names(plas) <- c('sample','contigs','size','gc','md5','repType','repTypeAcc','relaxase','relaxAcc',
  'mpf','mpfAcc','orit','oritAcc','mobility','closestMash','distance','id','clusterPri','clusterSec',
  'predHostRange1','predHostRange2','predHostRange3','obsHostRange','repHostRange','repHostRange2','assocPlas')
plas$sample <- gsub(".*\\:", "", plas$sample)
plas2 <- subset(plas, select = -c(md5,repType,repTypeAcc,relaxAcc,mpfAcc,distance,
  id, clusterPri,clusterSec,predHostRange1,predHostRange2, predHostRange3, obsHostRange,
  repHostRange,repHostRange2,assocPlas,orit,oritAcc))
knitr::kable(plas2) %>% kable_styling(full_width = T) 
```