https://github.com/thejmazz/ontoscope-phylify

Phylify module for Ontoscope
https://github.com/thejmazz/ontoscope-phylify

Last synced: 19 days ago
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Phylify module for Ontoscope

• Host: GitHub
• URL: https://github.com/thejmazz/ontoscope-phylify
• Owner: thejmazz
• Created: 2016-02-17T03:46:39.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2016-03-08T19:51:44.000Z (almost 9 years ago)
• Last Synced: 2024-11-07T08:51:34.790Z (2 months ago)
• Language: JavaScript
• Homepage: http://thejmazz.github.io/ontoscope-phylify/
• Size: 14.7 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# ontoscope-phylify

Phylify module for [Ontoscope]

[Ontoscope]: https://github.com/hyginn/Ontoscope

## Running

```bash

$ npm install

# in one tab

$ npm start

# in another tab

$ npm run serve

```

The bundle will recompile as you save, and the webpage will then automatically refresh.

R code is in `igraph`.

## Notebook

**2016/02/23** 

Webpage for streaming vertices into cytoscape.js. See [igraph](https://github.com/thejmazz/ontoscope-phylify/tree/106a2a8c0f17e82e8bfe86e5121f881d4719c87c/igraph) (at that commit). Has the first plot of FANTOM data!

**2016/02/26**

Integrated edges into cytoscape.js. Applied "cose" layout after all edges added. See [some pictures from the vacation](https://github.com/thejmazz/ontoscope-phylify/commit/c1541267798f946e7e66c20686a442962dd59373) (went to lag city). Next todo is to go back and get a nice plot from igraph.

**2016/02/27**

Cleaning, [nicer, circle, tree plots](https://github.com/thejmazz/ontoscope-phylify/tree/6db95b922b25ffee7accc0f26e90ca66a49d1946/igraph/plots)

**2016/02/28**

[Interactive plot with all nodes](https://github.com/thejmazz/ontoscope-phylify/raw/6775f541912d12db5d4400d1e94df9e79a460271/igraph/plots/plotly_01.png) at reasonable framerate with [plotly](https://github.com/ropensci/plotly/).

## Design Milestone

The PHYLIFY module sits near the top of the Ontoscope pipeline:

![screen shot 2016-02-16 at 10 49 28 pm](https://cloud.githubusercontent.com/assets/1270998/13099403/ba767692-d4ff-11e5-8815-82152481636e.png)

It is responsible for taking CO, which is the ontology of anatomical structures

and cells, from FANTOM, and building a useful graph out of it.

This graph will then be combined with FANTOM expression data, and through a

thresholding function, provide the cell types to use as background when

calculating differential expression with [DESeq2].

This module will take input data from the FANTOM cell ontology, which has been

downloaded and resides in this repository

[here](https://raw.githubusercontent.com/thejmazz/ontoscope-phylify/master/ff-phase2-140729.obo).

It will parse the `.obo` file using [bionode-obo] \(v0.1.0 at time of writing),

which is a streaming obo parser I have written that can take a URL or a file and

emit a stream of term objects, or newline delimited JSON (ndjson).

JSON can be easily interpreted into R data frames with [jsonlite], which also

supports streaming data.

The graph will be constructed using the relations present in the obo file. The

graph will be constructed using [graph.js] for the browser visualization tool,

and [igraph] for the actual data pipeline within R. It is valuable to have a

browser based interactive visualization, which you can toggle different

relations on/off, to get a feel for what the data represents, and the meanings

of the specific terms within the obo file.

[DESeq2]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html

[bionode-obo]: https://github.com/bionode/bionode-obo

[jsonlite]: https://cran.r-project.org/web/packages/jsonlite/index.html

[graph.js]: https://www.npmjs.com/package/graph.js

[igraph]: http://igraph.org/