Help with Creating Gene Diagram for Research Article

Question

[manuelmasrodriguez]

Hello:

I am in the process of writing a scientific article regarding the prevalence of mutations in the dystrophin gene of a certain population. I have all the data and wish to create a diagram similar to this one:

I want to display every patient's mutated segment over the dystrophin gene. I can do this with pen and paper but I don't know a simple way to do this on a computer. Any ideas?

Thanks,
Manuel

[manuelmasrodriguez]

My data is currently in Excel. For example, Patiient 1, Deletion, 45-46 (exons). The pie chart is not necessary. Will Inkscape allow me to make some sort of scale for each line? I can do this with a ruler stating each exon is 1mm perhaps, but don't know how to do it on a computer.

[Dan D]

Inkscape is very free-form. You can draw anything you want, however you want.

If you have programming knowledge, it would be worth a shot to generate the visualization with the help of a Cairo library for your language of choice.

[manuelmasrodriguez]

No programming language. So you believe Inkscape can give me something similar to this diagram?

[Dan D]

You can utilize Inkscape to create a diagram exactly like that one, yes. Vector illustration is your best bet if you don't have coding knowledge. It will allow you to specify the exact length and thickness of your lines. You can duplicate elements easily, and it's dead simple to correct mistakes. Use layers wisely and it will be a piece of cake.

[manuelmasrodriguez]

This is what I have so far:

[Dan D]

Looking good!

Answer 1

[Dan D]

Are you wanting to generate the diagram, or draw it using a vector illustration program like Adobe Illustrator?

If the former, you could make some pretty clear and compelling visualizations using IGV or IGB. If your data are in BAM or SAM then you're ready to roll with either of those two programs.

Adobe Illustrator is awesome but does cost money. Inkscape is a capable, free alternative.

EDIT: your first screencap didn't have that pie chart. Illustrator has tools to generate them. Don't know about Inkscape. You could also make one in Excel and import it into your drawing.

Answer 2

[Alex Paciorkowski]

For the location of the mutations in the gene, a combination of Scrible, [fancyGene][2], or maybe GSDS should get you there. If you have knowledge or interest in R, some of the image can probably be generated using genoPlotR. To be honest, I bet most people would draw something like this out in Adobe Photoshop or Illustrator or GIMP.

By the way, I would make the duplications blue, and deletions red since that is the convention for those events. The way it is illustrated now is confusing.

[2] http://bio.ieo.eu/fancygene/