The Genetic Map Comparator: a user-friendly application to display and compare genetic maps

January 18, 2017
By

(This article was first published on Blog – The R graph Gallery, and kindly contributed to R-bloggers)

The Genetic Map Comparator is an R Shiny application made to compare and characterize genetic maps. You can use it through the online version and read the related publication in Bioinformatics.

The biological perspective

A genetic map provides the position of genetic markers along chromosomes. Geneticists often have to visualize these maps and calculate their basic statistics (length, # of markers, gap size..). Multiple maps that share some markers have to be dealt with when several segregating populations are studied. These maps are compared to highlight their overall relative strengths and weaknesses (e.g. via marker distributions or map lengths), or local marker inconsistencies.

The Genetic Map Comparator is an effective user-friendly tool to complete these tasks. It is possible to upload your genetic maps and explore them using the various sheets accessible via links at the top of the window. The app provides example datasets, which makes it easy to understand its capacity in less than 2 minutes, so why not have a look?

 

The Dataviz perspective

This app highlights a few features of the power of shiny as a dataviz explorative tool:

  • The insertion of interactive charts (mainly using plotly) is straightforward
  • CSS can be applied, which gives a nice look to the app
  • It is easy to share the tool: in our case we installed it on our private shiny server, but the app is also usable from the github repository!
  • It is possible to load your files into the app, and export results really easily

If you want to see how to use these features, the code is freely available on github.

Example:

Here is a screenshot of the main tabs of the app:

 

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