Plot Reference (Mainly COSMIC) Signature Profile

show_cosmic_sig_profile(
  sig_index = NULL,
  show_index = TRUE,
  sig_db = "legacy",
  ...
)

Arguments

sig_index

a vector for signature index. "ALL" for all signatures.

show_index

if TRUE, show valid indices.

sig_db

default 'legacy', it can be 'legacy' (for COSMIC v2 'SBS'), 'SBS', 'DBS', 'ID' and 'TSB' (for COSMIV v3.1 signatures). For more specific details, it can also be 'SBS_hg19', 'SBS_hg38', 'SBS_mm9', 'SBS_mm10', 'DBS_hg19', 'DBS_hg38', 'DBS_mm9', 'DBS_mm10' to use COSMIC v3 reference signatures from Alexandrov, Ludmil B., et al. (2020) (reference #1). In addition, it can be one of "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ", "SBS_Nik_lab", "RS_Nik_lab" to refer reference signatures from Degasperi, Andrea, et al. (2020) (reference #2). UPDATE, the latest version of reference version can be automatically downloaded and loaded from https://cancer.sanger.ac.uk/signatures/downloads/ when a option with latest_ prefix is specified (e.g. "latest_SBS_GRCh37"). Note: the signature profile for different genome builds are basically same. And specific database (e.g. 'SBS_mm10') contains less signatures than all COSMIC signatures (because some signatures are not detected from Alexandrov, Ludmil B., et al. (2020)). For all available options, check the parameter setting.

...

other arguments passing to show_sig_profile.

Value

a ggplot object

Author

Shixiang Wang w_shixiang@163.com

Examples

show_cosmic_sig_profile()
show_cosmic_sig_profile(sig_db = "SBS")
show_cosmic_sig_profile(sig_index = 1:5)
show_cosmic_sig_profile(sig_db = "SBS", sig_index = c("10a", "17a"))

gg <- show_cosmic_sig_profile(sig_index = 1:5)
gg$aetiology