Question: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
30
gravatar for John
5.6 years ago by
John1.4k
John1.4k wrote:

Is there is any R package that can make similar circular plots as circos do ? I do use Perl so I love and use R packages . any hint is appreciated. .. .......

http://mkweb.bcgsc.ca/dev/circos/

R visualization • 17k views
ADD COMMENTlink modified 2.5 years ago by Mo810 • written 5.6 years ago by John1.4k

Related post at StackOverflow: Chord diagram in R

ADD REPLYlink written 9 months ago by zx87543.7k
13
gravatar for Kevin
5.6 years ago by
Kevin540
Kevin540 wrote:

check out http://www.r-bloggers.com/polar-histogram-pretty-and-useful/ it produces a circular plot sorta ..

ADD COMMENTlink written 5.6 years ago by Kevin540
10
gravatar for Sean Davis
4.6 years ago by
Sean Davis23k
National Institutes of Health, Bethesda, MD
Sean Davis23k wrote:

Late answer, but you might check out http://cran.r-project.org/web/packages/RCircos/.

ADD COMMENTlink written 4.6 years ago by Sean Davis23k
8
gravatar for Sean Davis
5.1 years ago by
Sean Davis23k
National Institutes of Health, Bethesda, MD
Sean Davis23k wrote:

Late answer, but check out the ggbio bioconductor package.

ADD COMMENTlink written 5.1 years ago by Sean Davis23k
7
gravatar for Zuguang Gu
4.2 years ago by
Zuguang Gu140
Germany
Zuguang Gu140 wrote:

well, another option is circlize, also available on CRAN

ADD COMMENTlink written 4.2 years ago by Zuguang Gu140
6
gravatar for Samir
3.7 years ago by
Samir120
United States
Samir120 wrote:

Checkout OmicCIrcos at R/Bioconductor. Vignette R script provides several good examples of drawing circular plots with couple of functionalities of popular Circos software, e.g., histogram, links and ribbons, heatmap, scatterplots.

ADD COMMENTlink written 3.7 years ago by Samir120
5
gravatar for Madelaine Gogol
5.6 years ago by
Madelaine Gogol4.8k
Kansas City
Madelaine Gogol4.8k wrote:

I've used radial.plot() from the plotrix package to make a radial plot, but it would take a lot of tweaking to get it to the circos level...

http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=75

Oh, are you also this person?

http://stackoverflow.com/questions/9417711/overlayed-circular-multiple-barcharts-in-r

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Madelaine Gogol4.8k
1

See I am already getting more useful hints than posting in stackoverflow - for example " visnab package"

ADD REPLYlink written 5.6 years ago by John1.4k

yes, but purpose of posting is here not only to create such graph but there are many more variations that can be created circos plots - trying to find some package can readily do it.

ADD REPLYlink written 5.6 years ago by John1.4k

That's fine, just making sure you got all the info.

ADD REPLYlink written 5.6 years ago by Madelaine Gogol4.8k
4
gravatar for Andrew Su
5.6 years ago by
Andrew Su4.7k
San Diego, CA
Andrew Su4.7k wrote:

From this question on the Bioconductor mailing list:

On Tue, Mar 8, 2011 at 2:50 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote:

You can check out Tengfei's visnab package. It's a package for interactive plotting of genomic data. It depends on the R/Qt infrastructure, and only really works on Linux and Mac right now. But it does have a nice looking circular view.

Grab it here: https://github.com/tengfei/VisNAB/

Hopefully in next release of Bioc.

Michael

Not much to look at in the github repository, but there are some images in this slide deck.

ADD COMMENTlink written 5.6 years ago by Andrew Su4.7k

from the slides this new package looks cool. Any doc on how we can use it now before it is part of the next BioC release

ADD REPLYlink written 5.6 years ago by Abhi1.4k
4
gravatar for Irsan
4.2 years ago by
Irsan6.3k
Amsterdam
Irsan6.3k wrote:

Rcircos is what you are looking for

ADD COMMENTlink written 4.2 years ago by Irsan6.3k
2
gravatar for mikhail.shugay
3.0 years ago by
mikhail.shugay3.2k
Czech Republic, Brno, CEITEC
mikhail.shugay3.2k wrote:

Thumbs up for Circlize, it was re-publised just recently (2014-09-01, see http://cran.r-project.org/web/packages/circlize/index.html ). After almost a week of unsuccessful attempts to run standalone Circos for representation of tabular data, I'm really satisfied by this package, which took me less than an hour to make it running. Moreover it is easy to generate a PDF output with vector graphics. So I recommend everyone more-or-less familiar with R to switch to it. The manual for this tool is also very helpful.

My five cents: check d3js, which provides lots of beautiful visualization utilities. This kind of plot is called Chord Diagram (e.g. http://strongriley.github.io/d3/ex/chord.html ). Those plots are interactive ones.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by mikhail.shugay3.2k
0
gravatar for hanguangchun
3.0 years ago by
hanguangchun120
United States
hanguangchun120 wrote:

haven't used it, but found some resources:

tutorial on omiccircos from here( in chinese)

introduction on rciros here

ADD COMMENTlink written 3.0 years ago by hanguangchun120
0
gravatar for yhu
2.5 years ago by
yhu50
United States
yhu50 wrote:

OmicCircos http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html

ADD COMMENTlink written 2.5 years ago by yhu50
0
gravatar for Mo
2.5 years ago by
Mo810
/
Mo810 wrote:

this can give you more or less the same plot https://gjabel.wordpress.com/2014/03/28/circular-migration-flow-plots-in-r/

ADD COMMENTlink written 2.5 years ago by Mo810
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