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vennt

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Dynamic Venn diagrams for differential gene expression

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# Vennt

* Dynamic Venn diagrams for exploring lists of differential expressed genes

Try a [Live Demo](https://drpowell.github.io/vennt/example/dge-example.html)

## Example Screenshot

![Vennt screenshot](https://drpowell.github.io/vennt/images/screenshot-1.png)

## Usage

### As a single HTML file

#### Using Cuffdiff output
Download this python script <a href='https://drpowell.github.io/vennt/dist/vennt.py'>vennt.py</a> (requires python >=2.7).  Then simply run:

python vennt.py --cuffdiff gene_exp.diff > my-vennt.html

This will create a single html file that can be shared.

#### Using a general CSV file

Generate a single CSV file with all your gene lists.  Each row of the CSV should contain information about a gene including the `log fold change`, and the `adjust p-value`.  Use a single column to specify the gene-list (see the example below).  Each gene must have a unique identifier, which is used to find the corresponding genes in the different gene lists.

Download this python script <a href='https://drpowell.github.io/vennt/dist/vennt.py'>vennt.py</a> (requires python >=2.7).  Then, if your CSV column names match the defaults, simply run it as follows:

python vennt.py gene-lists.csv > my-vennt.html

You may specify alternative column names, see `python vennt.py -h` for help.  And read the settings list below for more information on the columns.

### With the CSV file from a webserver

Creating a single HTML file with all your gene lists embedded may be a problem due to the size of the resulting HTML file.  In that situation, you can serve the gene-list CSV file from a web-server.  Firstly, create your CSV as described above.

Download this <a href='https://drpowell.github.io/vennt/example/template.html'>html file</a>.  Then, put it and your CSV file on a web-server.  (For local testing you can use `python -mSimpleHTTPServer`.)

You may need to specify some configuration if the defaults do not suffice, for example column names.  These are configured in the html file.

#### Available settings

Set these in `window.venn_settings` in your html file (or using the options to vennt.py).

* `csv_file`  - (default 'data.csv') Name of the CSV file containing the data to load.  Must be on the same origin as the html file due to javascript's [Same-origin policy](http://en.wikipedia.org/wiki/Same-origin_policy) 
* `csv_data` - (default 'null') - This can be used to directly embed a CSV file rather than requesting via ajax.  Note, setting this parameter will cause any `csv_file` to be ignored
* `key_column` - (default 'key') Name of the column specifying the gene-list.
* `id_column` - (default 'Feature') Name of the column specifying a unique identifier for the gene.  This must be unique within each gene-list, because it is used to match up the genes between the different gene-lists.
* `fdr_column` - (default 'adj.P.Val') - Name of the column containing the adjusted p-value.  (This is often a false-discovery rate.)
* `logFC_column` - (default 'logFC') - Name of the column containing the log-fold-change for each gene-list.
* `info_columns` - (default '[Feature]') - An array of column names to display to the user.  This should contain useful information you want the user to see - such as a gene-id, perhaps common gene-name, or possibly a brief description.
* `show_tour` - (default true) - Show the Venn tour on page load (if not shown before)

For example, consider this is your csv file, which is called `data.csv`:

gene-list,id,Description,Gene Name,logFC,adj.P.Val
    WT vs MT1,ENSG00000083520,DIS3 mitotic control homolog (S. cerevisiae),DIS3,-2.4,4.8e-10
    WT vs MT1,ENSG00000025156,heat shock transcription factor 2,HSF2,-0.89,6.4e-05
    WT vs MT1,ENSG00000103042,"solute carrier family 38, member 7",SLC38A7,1.5,6.4e-05
    WT vs MT2,ENSG00000083520,DIS3 mitotic control homolog (S. cerevisiae),DIS3,-2.4,4.8e-10
    WT vs MT2,ENSG00000025156,heat shock transcription factor 2,HSF2,-0.89,6.4e-05
    WT vs MT2,ENSG00000103042,"solute carrier family 38, member 7",SLC38A7,1.5,6.4e-05

You would specify this in your html file:

window.venn_settings = { csv_file: 'data.csv',
                             key_column: 'gene-list',
                             id_column: 'id'
                             info_columns: ['id', 'Description', 'Gene Name']
                           }

or using `vennt.py`

python vennt.py data.csv --key gene-list --id id --info id Description 'Gene Name'

## Contributing ##
Feel free to contribute with pull requests, bug reports or enhancement suggestions.

## Development

### To build 
For building from sources, you will need nodejs and the following modules.

npm install -g browserify
    npm install -g clean-css
    npm install hbsfy@1.3
    npm install handlebars-runtime
    npm install coffeeify       # Needs to be local?

# Builds files index.html, main.js, main.min.css into build/
    ./build.sh

### For development
This will watch the js & coffeescript files and rebuild `main.js` as needed.  You'll still need to build the css using `build.sh`.

npm install -g watchify

watchify -t coffeeify -t hbsfy --debug app/main.coffee -o build/main.js -v
    (cd build ; python -mSimpleHTTPServer)

## License ##
Vennt is released under the GPL v3 (or later) license, see <a href='https://github.com/drpowell/vennt/blob/master/COPYING.txt'>COPYING.txt</a>

vennt

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