[R] Need in formatting data for circos plot

[pooja sinha]

Thanks, the code is working now but it is not plotting in the colorwise
manner ie, khaki4 and indian red. Maybe I need to work more. If you have
any clue then please let me know.


Thanks again,
Puja

On Tue, Oct 5, 2021 at 9:19 AM PIKAL Petr <petr.pikal using precheza.cz> wrote:

> Hm,
>
> Maybe if you change
> > C(-7, 7)
> Error in C(-7, 7) : object not interpretable as a factor
>
> to
>
> > c(-7, 7)
> [1] -7  7
>
> Cheers
> Petr
>
>
> S pozdravem | Best Regards
> RNDr. Petr PIKAL
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> > -----Original Message-----
> > From: R-help <r-help-bounces using r-project.org> On Behalf Of pooja sinha
> > Sent: Tuesday, October 5, 2021 2:20 PM
> > To: r-help mailing list <r-help using r-project.org>
> > Subject: [R] Need in formatting data for circos plot
> >
> > Hi All,
> >
> > I have gene expression data with differential fold change value and the
> file
> > looks like as below:
> > Chrom start_pos end_pos value
> > 14 20482867 20496901 2.713009346
> > 4 123712710 123718202 -2.20797815
> > 13 80883384 80896042 1.646405782
> > 16 48842551 48844461 -1.636002557
> > 17 28399094 28517527 1.033066311
> > 9 31846044 31913462 -1.738549101
> > 1 45311538 45349706 -1.360867536
> > I wrote a code in R but it is giving error so I need help in trouble
> > shooting:
> > library(circlize)
> > library(gtools)
> > library(dplyr)
> > circos.initializeWithIdeogram(species = "mm10")
> > circos.par("track.height"=0.20)
> >
> > circos.genomicTrackPlotRegion(data = db_tr,ylim = C(-7, 7),
> numeric.column
> > = 4,
> >                               panel.fun = function(region,value,...) {
> >                                 cond <- value[,1] < 0.0
> >                                 circos.genomicPoints(region[cond,],
> > value[cond,], pch = ".", cex = 0.1,
> >                                                      col = "khaki4")
> >                                 circos.genomicPoints(region[!cond,],
> > value[!cond,], pch = ".", cex = 0.1,
> >                                                      col = "indianred")
> >                               })
> > Error is : Error in C(-7, 7) : object not interpretable as a factor
> >
> > Please help as I am new to circos plot and tried a lot. The file is also
> attached
> > here.
> >
> > Thanks,
> > Puja
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