---
title: "Use a Stock Genome"
author: "Paul Shannon"
package: igvR
date: "`r Sys.Date()`"
output:
   BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{"Use a Stock Genome"}
  %\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

[igv.org](https://igv.org/) currently (July 2022) provides 35 common and model organism
annotated genomes.   Each of these is easily specified and used in igvR

When igvR is initialized communication is established between your R session and your default
web browser.  Then, in a separate function call, you specifies the genome of interest.
igvR then renders the genome browser view and interactive navigation can begin.

# Demonstration

```{r eval=FALSE}
library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "Stock Genomes")
print(sort(getSupportedGenomes(igv)))
```

```
ASM294v2 ASM985889v3  bosTau8 bosTau9  canFam3 canFam5  ce11 chm13v1.1
chm13v2.0 danRer10 danRer11 dm3  dm6 dmel_r5.9 galGal6 GCA_003086295.2
gorGor4 gorGor6 hg18 hg19 hg38  hg38_1kg macFas5 mm10 mm39 mm9 panPan2
panTro4 panTro5 panTro6 rn6 rn7 sacCer3 susScr11 tair10
```

```{r eval=FALSE}
setGenome(igv, "hg38_1Kg")
showGenomicRegion(igv, "APOE")
zoomOut(igv)

```


# Display

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

# Session Info

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