ggbio package only works with h19 genome
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tiago211287 ▴ 10
@tiago211287-9049
Last seen 8 months ago
Brazil

Someone here knows how to use the bioconductor ggbio package for plotting ideograms?

in the manual it says : 

"Ideogram provides functionality to construct ideogram, check the manual for more flexible methods. We build genome hg19, hg18, mm10, mm9 inside, so you don’t have download it on the fly. "

library(ggbio) p.ideo <- Ideogram(genome = "hg19")

p.ideo

But when I replace the h19 to mm10 in the code bellow, I get an error :

> p.ideo <- Ideogram(genome = "mm10")
use chr1 automatically
Error in ifelse(nrow(df.tri.p2), list(do.call(geom_arch_flip2, c(list(data = df.tri.p2),  : 
  erro na avaliação do argumento 'yes' na seleção do método para a função 'ifelse': 'Error in eval(expr, envir, enclos) : object 'y' not found

Can someone help me?

ggbio ggplot2 • 1.1k views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States

The short answer is that Ideogram() calls layout_karyogram(), which is hard-coded to look for the 'acen' stain in the data, in order to set up the p and q arms. But since the mouse has only telocentric chromosomes, there is no acen stain, so you get the error you see.

Given that the problem is hard-coded, I don't think there is an easy answer, but perhaps the 'flexible methods' in the manual would be helpful?

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