R/show_cn_freq_circos.R
show_cn_freq_circos.Rd
Show Copy Number Variation Frequency Profile with Circos
show_cn_freq_circos( data, groups = NULL, cutoff = 2L, resolution_factor = 1L, title = c("AMP", "DEL"), chrs = paste0("chr", 1:22), genome_build = c("hg19", "hg38", "mm10", "mm9"), cols = NULL, plot_ideogram = TRUE, track_height = 0.5, ideogram_height = 1, ... )
data | a |
---|---|
groups | a named list or a column name for specifying groups. |
cutoff | copy number value cutoff for splitting data into AMP and DEL.
The values equal to cutoff are discarded. Default is |
resolution_factor | an integer to control the resolution.
When it is |
title | length-2 titles for AMP and DEL. |
chrs | chromosomes start with 'chr'. |
genome_build | genome build version, used when |
cols | length-2 colors for AMP and DEL. |
plot_ideogram | default is |
track_height | track height in |
ideogram_height | ideogram height in |
... | other parameters passing to circlize::circos.genomicLines. |
Nothing.
# \donttest{ 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")) # }