[R] Problems in writing code for circos plot

[Bert Gunter]

Wrong list -- (for which statistical methods question are generally
offtopic anyway).

Post here instead:
https://www.bioconductor.org/help/

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Feb 17, 2020 at 6:58 AM pooja sinha <pjsinha07 using gmail.com> wrote:

>  Hi All,
>
>
> I had previously mentioned that I have large data set with methylation
> values ranging from 0-1. The data contains around 3 million rows of values
> corresponding to the chromosomal locations. I want to split/sort my data
> for plot using circos plot. I thought of doing like sorting the value range
> 0.2-0.4 as hypomethylation category and range 0.7-1.0 as hypermethylation
> category. However, with this approach the plot again looks cluttered.
> Another way is that I can split the data into two parts, one part with
> values lower than median, and another part with values larger than median.
>
> Can anyone suggest me which approach is better or if there are other
> approaches I can use in my datasets for circos plot using circlize package.
>
>
> Thanks,
>
> Puja
>
> On Sun, Jan 26, 2020 at 5:06 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> > Hi Puja,
> > Three things:
> > 1) Your data files are very large. If you do manage to get circular
> > plots out of them with the circlize library they will probably be very
> > dense.
> > 2) The structure of your data includes too many levels in "Chrom" to
> > get the circlize functions to work. I had to pare them back to the
> > non-random levels.
> > 3) You should probably change the subject line of your message to
> > "Would anyone care to do my work for me?"
> >
> > Jim
> >
> > On Mon, Jan 27, 2020 at 6:47 AM pooja sinha <pjsinha07 using gmail.com> wrote:
> > >
> > > Hi All,
> > >
> > > I have attached the three different datasets for Rn6 genome (rat) and I
> > > needed to use circos plot by *circlize package in R*. Please anyone
> help
> > me
> > > in writing the code and making the plot. Any help will be highly
> > > appreciated.
> > > The three file links are below:
> > >
> > > File 1: YOUNGCONTROL.csv (
> > > https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 )
> > > File 2:  YOUNGTREATED.csv (
> > > https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO )
> > > File 3:  YOUNGTREATED.vs.YOUNGCONTROL.sig.csv (
> > >
> >
> https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN
> > >  )
> > >
> > > The circos plot having the outermost ring contain Rn6 ideogram followed
> > by
> > > YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of
> > > YOUNGTREATED.vs.YOUNGCONTROL.sig
> > >
> > > Thanks,
> > > Puja
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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