Question: how to plot human genome chromosome Ideogram with each length by Gviz
1
gravatar for dulunar
2.7 years ago by
dulunar10
dulunar10 wrote:

Hello, guys,

  I used Gviz for plotting human genome chromosome ideogram in one picture together, but when I get the picture, I find the width of each chromosome is similar, for example: 

http://photo.weibo.com/2512269257/wbphotos/large/mid/4078500543856337/pid/95be2fc9ly1fd0yepd5x6j21eu07s0tp

 

but I want to get the picture like this : 

http://photo.weibo.com/2512269257/wbphotos/large/mid/4078500543856337/pid/95be2fc9ly1fd0yer7gn8j218m07oq3y

what should I do?

 

Thanks!

 

ideogram gviz chromosome • 1.4k views
ADD COMMENTlink modified 2.7 years ago by bernatgel120 • written 2.7 years ago by dulunar10
Answer: how to plot human genome chromosome Ideogram with each length by Gviz
0
gravatar for florian.hahne@novartis.com
2.7 years ago by
Switzerland

Not sure what these links are supposed to show, but for me they only get me to some Chinese photo sharing page.

From the vague description in the text I gather that you want to plot all human chromosomes through Gviz in their relative size. That is not possible, and Gviz is not designed to do that. Ideograms in Gviz are really just a special type of track objects. You may want to look into more general purpose graphics to do that.

Florian

ADD COMMENTlink written 2.7 years ago by florian.hahne@novartis.com1.6k

Thank You,  I get it!

ADD REPLYlink written 2.7 years ago by dulunar10
Answer: how to plot human genome chromosome Ideogram with each length by Gviz
0
gravatar for James W. MacDonald
2.7 years ago by
United States
James W. MacDonald51k wrote:

An alternative to Gviz that will do different length karyograms is ggbio. For an example see here.

But do note that the original author of ggbio has moved on and no longer supports it, so you won't get the level of support that people get for Gviz.

ADD COMMENTlink written 2.7 years ago by James W. MacDonald51k

Thank you, i am try to use this package~

ADD REPLYlink written 2.7 years ago by dulunar10
Answer: how to plot human genome chromosome Ideogram with each length by Gviz
0
gravatar for bernatgel
2.7 years ago by
bernatgel120
Spain
bernatgel120 wrote:

You can use karyoploteR for that. You can create the complete ideograms for many different genomes (even for custom ones) and plot data on it if you want.

IMPORTANT: karyoploteR is only available in Bioconductor devel until next release (mid April 2017)

To create a simple ideogram of the human genome version hg19 you only need

    library(karyoploteR)
    plotKaryotype()

and it will create a plot like this

Ideogram of the human genome

 

 

ADD COMMENTlink written 2.7 years ago by bernatgel120
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