layout_circle using ggbio pulling data from a .csv

Question

I'm trying to pullout the data of my chromosome size which is stored on a .csv. Went I try to graph that information I get the next error: "Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'layout_circle' for signature '"data.frame"

This is what I'm using:

library(ggbio)
ChrLen2 = read.csv("ChrLen2.csv") #Change name of the file
p <- ggplot() + layout_circle(ChrLen2, geom = "ideo", fill = "gray70",
                              radius = 30, trackWidth = 4)

Is there a way I can call a file into my code?

In advance, thank you!

Answer 1

Check the help manual for ggbio, you need to provide a GRanges object to plot, and within it you specify the chromosome length information, for example:

library(ggbio)
library(GenomicRanges)

gr = GRanges(seqnames="chr2",IRanges(start=1 ,end= 1))

seqinfo(gr)

Seqinfo object with 1 sequence from an unspecified genome; no seqlengths:
  seqnames seqlengths isCircular genome
  chr2             NA         NA   <NA>

seqlengths(gr) = 2e6

seqinfo(gr)
Seqinfo object with 1 sequence from an unspecified genome:
  seqnames seqlengths isCircular genome
  chr2        2000000         NA   <NA>

ggplot() + layout_circle(gr, geom = "ideo", fill = "gray70",
                              radius = 30, trackWidth = 4)