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How To Draw A Chromosome With Gene Positions Marked

Dear all, I need to draw a graph of a specific chromosome with each gene marked on it. An examplified gene list is as shown below.

gene    chromosome  start   end
Act-1   I           20      2000
Atp-1   I           3000    4000
Kin-4   I           6000    8000
...........................

i can't figure out how to draw it using R (I am R beginner). It's easy to transform the above data to the following one.

gene    chromosome  start   gene_width
Act-1   I           20      1980
Atp-1   I           3000    1000
Kin-4   I           6000    2000
...........................

I think it is a histogram, but different gene has different width. Could anyone help to solve this problem? I believe this is a very common question for many bioinformatics beginners.

Thanks a lot!

r chromosome
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updated by jackuser1979 jackuser1979 • written by biolab biolab

thank you very much for your information!

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written by biolab biolab

You are very welcome to post again if you have a question about a specific tool, visualization or library.

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written by Michael Dondrup Michael Dondrup

Thanks, Mike, i take a look at those R packages and Genome Browser. I want to ask you again. My task actually is simple, just mark genes on a chromosome. Could you please give me your suggestions on the simplest way to draw a chromosome marked with genes (actually i only need to mark ~500 genes, my problem is that i don't know how to draw according to their width). Thanks again.

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written by biolab biolab

I think if you intend to make drawings of chromosome ideograms and data in R, prettiest graphics (subjective) are currently produced by the Gviz package, also getting the ideogram data is fairly automatised, if available. ofc there is a little learning of R and datastructures involved. I recommend that you browse through the documentation and examples and see if you can figure out how to do the data import and drawing. http://www.bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.pdf contains in its first example a graphic of such an ideogram plot.

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written by Michael Dondrup Michael Dondrup

Hi Mike, Gviz is really good. I am reading the manual and hopefully can draw a nice graph using it. If there are further questions, i will post in biostars. Thank you!

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written by biolab biolab

Hello, Mike. If I just like to mark genes or some segments instead on the chromosome figure but not its ideogram, what packages should I use? Can Gviz generate the non-ideogram version of a chromosome?

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written by zy041225 zy041225

1 answer

You can make use of ArkMAP to map your genes on chromosome.

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written by jackuser1979 jackuser1979

thanks a lot for providing the webtool.

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written by biolab biolab

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