Closed rajeha closed 1 year ago
@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"))
Super helpful - thanks!
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!