How To Visualize Custom 2D Genomic Data In A Genome Browser?

Question

[TFTF]

There is a large array of different genome browsers, each with its own characteristics. Obviously a lot of work has been put into developing these. However, I was surprised that I could not find any genome browser that supports visualization of 2d genomic data as well as 1d genomic data (genomic tracks). Does anyone know of such genome browsers?

By 2d genomic data I mean any quantitative data which is assigned to pairs of genomic locations, and would often be visualized as a heatmap (as Istvan suggested, this can be also interpreted as 3d data). An example of 2d genomic data would be calculation of linkage disequilbrium between pairs of loci. This is just one example of 2d data, I want to be able to visualize my own 2d datasets (not LD) in parallel.

I would prefer a fast offline genome browser (not web-based) with extensive customization options, if such a browser exists.

Thanks

[Istvan Albert]

genomic coverage data is two dimensional (coordinates have values) and those can be visualized in existing browsers. So your title is a little bit misleading - you should make it more specific to what you are looking for so that people can help you with advice. - later: edited your title

[TFTF]

@Istvan I gave LD data as an example of 2d data, I want to be able to upload multiple arbitrary 2d data sets and show them. I explicitly explained what I mean by 2d, but I have now clarified that further. Thanks.

Answer 1

[Leandro Lima]

Do you mean LD plot like this? http://www.ensembl.org/Homo_sapiens/Location/LD?db=core;focus=variation;pop1=1000GENOMES:phase_1_ASW;r=22:25845459-25865458;v=rs12345;vdb=variation;vf=13424

Here is an example of search in Ensembl website, with SNP rs12345. http://www.ensembl.org/Homo_sapiens/Variation/HighLD?db=core;r=22:25854959-25855959;v=rs12345;vdb=variation;vf=13424

[TFTF]

Thanks, this is exactly what I am looking for, but does the ensembl browser support uploading custom 2d data? Also, do you know if there is a local/offline version?

Answer 2

[Michael]

I think Haploview is one of the top-rated applications to do this. If you search google for images with "linkage disequilibrium plot" then most of the images look like coming from Haploview.

[TFTF]

Thanks, I have played with Haploview a bit before. Do you know if it supports upload of custom (non LD) data and whether it can show 1d and 2d multiple datasets in parallel?

Answer 3

[Alex Reynolds]

Another option is a Circos plot, connecting two genomic regions (first dimension) with an arc of varied color or thickness (second dimension). It's very customizable, at the expense of having to write scripts to glue your data to the rendering script.

[TFTF]

Thanks, this is good to know. Unfortunately it does not fit well the type of datasets and comparisons that I had in mind.