[R] Problems in writing code for circos plot

[pooja sinha]

 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]]
> >
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