show_cn_freq_circos() y axis

[rajeha]

Hi @ShixiangWang,

I hope you are doing well! Would you please clarify what the y-axis of the show_cn_freq_circos() function output represents? It is not clear in the documentation.

Thank you!

[ShixiangWang]

@rajeha

This function draws copy number amplification and deletion across the genome, you can check the example code. For a specific region, the height shows the proportion with AMP/DEL in all samples. If you provide a group list, each group will be drawn and the ratio will be calculated separately. (The reference, i.e., normal copy number is 2, >2 is defined as AMP, <2 is defined as DEL)

For example code:

load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))

show_cn_freq_circos(cn)

ss <- unique(cn@data$sample)
show_cn_freq_circos(cn, groups = list(a = ss[1:5], b = ss[6:10]), cols = c("red", "green"))

[rajeha]

Super helpful - thanks!