Question: (Closed) How To Draw A Chromosome With Gene Positions Marked
0
gravatar for biolab
4.6 years ago by
biolab1000
biolab1000 wrote:

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 • 13k views
ADD COMMENTlink modified 4.6 years ago by jackuser1979850 • written 4.6 years ago by biolab1000
3

yes, it is a common question and has therefore been answered multiple times before. see: Drawing chromosome ideogams with data or What tools/libraries do you use to visualize genomic feature data? or how to draw genome features along chromosome and Packages for visualization of biological data in R,

ADD REPLYlink written 4.6 years ago by Michael Dondrup44k

thank you very much for your information!

ADD REPLYlink written 4.6 years ago by biolab1000

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

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Michael Dondrup44k

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.

ADD REPLYlink written 4.6 years ago by biolab1000

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.

ADD REPLYlink written 4.6 years ago by Michael Dondrup44k

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!

ADD REPLYlink written 4.6 years ago by biolab1000

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?

ADD REPLYlink written 3.6 years ago by zy04122560
2
gravatar for jackuser1979
4.6 years ago by
jackuser1979850
US
jackuser1979850 wrote:

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

ADD COMMENTlink written 4.6 years ago by jackuser1979850

thanks a lot for providing the webtool.

ADD REPLYlink written 4.6 years ago by biolab1000
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