dng-mutmap's Introduction

This repository is a sort of "plugin" for denovogear. It adds the mutmap command to dng, which allows the generation of an HTML file which contains an interactive visualization.

Installation

Copy everything in this repository (except this README file) into the root of your denovogear repository.

You also need to add the following line to src/CMakeLists.txt:

add_subdirectory(mutmap)

There are also some runtime dependencies. You'll need to have R installed (specifically the Rscript command), along with the R libraries listed in src/mutmap/tools/install_r_dependencies.R.

Once everything is in place, rebuild and install denovogear. You should now have the dng mutmap command available.

Running

You need 2 things to generate the visualization file:

A VCF file as output from a denovogear run
A corresponding ped file for the pedigree matching the VCF

Then you can run something like the following:

dng mutmap -p PED_FILE.ped -d DNG_OUTPUT_FILE.vcf -o mutmap.html

You should then be able to open the mutmap.html file in any modern browser to see the visualization. Note that currently the entire contents of the VCF file is included in the HTML file, so it can be quite large and take a bit of time to load, especially if you host the HTML file over the internet. This has only been tested with a ~20MiB file so far.

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dng-mutmap's Issues

Server cannot handle pedigree files with blank lines at end

Parse ped file in javascript

Probably necessary to handle newick trees

Handle ped files with missing 6th column

If newick tree isn't present should use the ID as the library name.

Remove backend server

What we want is for denovogear to generate an HTML file that includes all the pedigree and layout information embedded directly. This simplifies the user interface (user doesn't have to upload files) and more tightly integrates the visualization with that specific run of denovogear, which gives us more control for validation, etc.

Since we're using R as a dependency on the server for calculating the layout, we can change that to be a direct dependency for denovogear and compute the layout directly on the client.

It's ok to still call out to static servers for javascript libraries, etc.