# igvR
igvR is an R package providing interactive connections to
[igv.js](https://github.com/igvteam/igv.js/tree/master)
(the Integrative Genomics Viewer) running in a web browser.
I am grateful to Jim Robinson, Helga Thorvaldsdóttir, Douglass Turner and
colleagues for their fine work in igv.js, and their unfailing
responsiveness to all requests and questions.
igvR is based upon the Bioconductor R package
[BrowserViz](https://paul-shannon.github.io/BrowserViz/) - of which it
is a subclass. It offers easy interactive visual exploration of
genomic data from R:
- Bed (annotation) and BedGraph (quantitative)
tracks can be created out of **_R_** data.frames and GenomicRanges
objects.
- Aligment data from bam files via GAlignments objects offered by
the GenomicAlignments class
- variant data from VCF files via VCF objects offered by the
VariantAnnotation class.
This work is motivated by our belief that contemporary web browsers,
supporting HTML5 and Canvas, and running increasingly powerful
Javascript libraries (for example, d3, igv.js and cytoscape.js) have become
the best setting in which to develop interactive graphics for
exploratory data analysis.
Here, for example, we display a BAM pileup from a ChIP-Seq experiment, accompanied by narrow
peaks called by MACS2, and TF motif matches from MotifDb to sequence
scored by the Bioconductor's Biostrings::matchPWM, and showing a
browser popup with the motif logo associated with the transcription
factor CTCF, obtained by clicking on a region displayed in the lowest
track.
Code for this example is in the vignette titled
```
"Explore ChIP-seq alignments from a bam file, MACS2 narrowPeaks, conservation, methylation
and motif matching"
```
## set up a minimal webserver to host your own large genomic files
The python flask webserver, with an additional *CORS* module, is all
you need.
1. python version >= 3
2. requirements.txt, with two lines:
Flask
flask_cors
3. the following simple web server code
```
from flask import Flask
from flask_cors import CORS
app = Flask(__name__, static_url_path='/static')
CORS(app)
@app.route('/')
def serveStaticFiles():
return 'CORS and byte-range request flask webserver (dockerized) for igvR and igvShiny (16 jul 2021)\n'
if __name__ == "__main__":
app.run(host='0.0.0.0', port='60050')
```
