Question: Help with Creating Gene Diagram for Research Article
1
gravatar for manuelmasrodriguez
4.9 years ago by
manuelmasrodriguez10 wrote:

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

gene • 3.4k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.9 years ago by manuelmasrodriguez10

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.

ADD REPLYlink written 4.9 years ago by manuelmasrodriguez10

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.

ADD REPLYlink written 4.9 years ago by Dan D6.8k

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

ADD REPLYlink written 4.9 years ago by manuelmasrodriguez10

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.

ADD REPLYlink written 4.9 years ago by Dan D6.8k

This is what I have so far:

[IMG]http://i.imgur.com/KZl6UAZ.jpg[/IMG]

 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by manuelmasrodriguez10

Looking good!

ADD REPLYlink written 4.8 years ago by Dan D6.8k
0
gravatar for Dan D
4.9 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

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.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Dan D6.8k
0
gravatar for Alex Paciorkowski
4.9 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

For the location of the mutations in the gene, a combination of Scrible, fancyGene, 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.

ADD COMMENTlink written 4.9 years ago by Alex Paciorkowski3.3k
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