[R] Need in formatting data for circos plot

[PIKAL Petr]

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
Vedoucí Výzkumu a vývoje | Research Manager
PRECHEZA a.s.
nábř. Dr. Edvarda Beneše 1170/24 | 750 02 Přerov | Czech Republic
Tel: +420 581 252 256 | GSM: +420 724 008 364
petr.pikal using precheza.cz | www.precheza.cz
Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních
partnerů PRECHEZA a.s. jsou zveřejněny na:
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about
processing and protection of business partner's personal data are available
on website: https://www.precheza.cz/en/personal-data-protection-principles/
Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné
a podléhají tomuto právně závaznému prohlášení o vyloučení odpovědnosti:
https://www.precheza.cz/01-dovetek/ | This email and any documents attached
to it may be confidential and are subject to the legally binding disclaimer:
https://www.precheza.cz/en/01-disclaimer/

> -----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
> ______________________________________________
> 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.