---
title: "Paired-end Interaction Tracks"
author: "Paul Shannon"
package: igvR
date: "`r Sys.Date()`"
output:
   BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{"Paired-end Interaction Tracks"}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

<style>
.main-container { width: 1000px; max-width:2800px;}
</style>


```{r setup, include = FALSE}
options(width = 120)
knitr::opts_chunk$set(
   collapse = TRUE,
   eval = interactive(),
   echo = TRUE,
   comment = "#>"
)
```


# Overview

With the popularity and wide availability of [Hi-C](https://en.wikipedia.org/wiki/Hi-C_(genomic_analysis_technique)) data -
a high throughput chromatin confirmation capture technology - an appropriate display format was needed.  The igv.js team
created the [Interact](https://github.com/igvteam/igv.js/wiki/Interact) track, supporint the
[bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) data file format.

# Example
We demonstrate this track with a few lines extracted from the Encode project's
[ENCFF110BUX](https://www.encodeproject.org/search/?type=Experiment&searchTerm=ENCFF110BUX) experiment,
from Michael Snyder's lab, showing the boundaries and extent of two topologically-associated domains (TADS),
typically small genomic regions which are somewhat isolated from neighboring regions, which is believed to play a role in restricting
enhancer/promoter interactions.

An equally important, and perhaps more common use of paired-end interaction data is to represent Hi-C maps of
enhancer-promoter interactions.   These data also rely upon the *bedpe* file format.

igv.js provides several visualization parameters not yet supported in igvR.

To define a TAD, two genomic locations are required, as shown here and in the code below:

```
      chrom1    start1      end1 chrom2    start2      end2
           2 105780000 105790000      2 105890000 105900000
           2 105575000 105600000      2 106075000 106100000
```
# Code

These few lines provide a complete, if minimal introduction to the *BedpeInteractionsTrack*.

```{r eval=FALSE}
library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "Paired-end demo")
setGenome(igv, "hg38")
tbl.bedpe <- data.frame(chrom1 = c("2", "2"),
                        start1 = c(105780000, 105575000),
                        end1 = c(105790000, 105600000),
                        chrom2 = c("2", "2"),
                        start2 = c(105890000, 106075000),
                        end2 = c(105900000, 106100000),
                        stringsAsFactors = FALSE)

  # construct a "region of interest" (roi) string from tbl.bedpe
  # this is where our two features are found.

shoulder <- 300000
roi <- sprintf("%s:%d-%d", tbl.bedpe$chrom1[1],
                           min(tbl.bedpe$start1) - shoulder,
                           max(tbl.bedpe$end2) + shoulder)

showGenomicRegion(igv, roi)
track <- BedpeInteractionsTrack("ENCFF110BUX", tbl.bedpe)
displayTrack(igv, track)
```

# Display

```{r, eval=TRUE, echo=FALSE, out.width="95%"}
knitr::include_graphics("pairedEnd.png")
```


# Session Info

```{r eval=TRUE}
sessionInfo()
```

