---
title: 'Dowser: Simple lineage tree construction'
author: "Kenneth B. Hoehn"
date: '`r Sys.Date()`'
output:
  pdf_document:
    dev: pdf
    fig_height: 4
    fig_width: 7.5
    highlight: pygments
    toc: yes
  html_document:
    fig_height: 4
    fig_width: 7.5
    highlight: pygments
    theme: readable
    toc: yes
  md_document:
    fig_height: 4
    fig_width: 7.5
    preserve_yaml: no
    toc: yes
geometry: margin=1in
fontsize: 11pt
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{Quickstart}
  %\VignetteEncoding{UTF-8}
  %\usepackage[utf8]{inputenc}
---

Quick start of lineage tree reconstruction.

```{r, eval=FALSE, warning=FALSE, message=FALSE}
# Load required packages
library(alakazam)
library(dowser)

# load example AIRR tsv data
data(ExampleAirr)

# subset data for this example 
# only one clone used for speed, otherwise can include multiple clones
ExampleAirr = ExampleAirr[ExampleAirr$clone_id %in% c("3170"),]

# Process example data into proper format, store isotype (optional)
clones = formatClones(ExampleAirr, traits="c_call")

# Build maxmimum parsimony trees for first clone using 
# phangorn package in R
trees <- getTrees(clones)

# simple tree plotting with ggtree R package with isotypes at tips
plots <- plotTrees(trees, tips="c_call",tipsize=2)

# plot tree of largest clone
plots[[1]]
```

