Chapter 8 Signature Object
Signature is a core object in sigminer, it stores signatures and their exposures. Here we show how to plot signature profile and exposure profile. The result plots are basically ggplot based, so they can be further edited by your custom operations with ggplot grammar.
8.1 Signature Profile
A signature is composed of distinct component patterns. They can be shown by
show_sig_profile(). Of note, for different types of signature, the bar heights may have different meanings.
- SBS signatures are displayed based on the observed component frequency of the human genome, i.e., representing the relative proportions of mutations generated by each signature based on the actual trinucleotide frequencies of the reference human genome.
- Similar to SBS signatures, copy number signatures are displayed based on the observed component frequency of the human genome. Of note, considering the count process of each feature is relatively independent, the profile is row normalized by each feature, unlike Macintyre et al. (2018) did column normalization (this method is easy to mislead readers), so the bar height can be compared within/between features.
8.1.1 SBS Signature profile
8.1.2 Copy Number Signature Porfile
For copy number signatures from tally method “W”, you have to specify the
normalize option as “feature”, so the bar heights can be more clearly compared.
8.1.3 COSMIC Signature Profile
Users can show profile of COSMIC signatures by
To see valid signature numbers, run
‘legacy’ is for COSMIC v2.
To show the plot, specify signature shortnames to
8.2 Exposure Profile
You can put group labels in the exposure profile.
grp <- get_groups(sig_w) #> [36mℹ[39m [2020-10-09 00:03:40]: Started. #> [32m✓[39m [2020-10-09 00:03:40]: 'Signature' object detected. #> [36mℹ[39m [2020-10-09 00:03:40]: Obtaining clusters from the hierarchical clustering of the consensus matrix... #> [36mℹ[39m [2020-10-09 00:03:40]: Finding the dominant signature of each group... #> => Generating a table of group and dominant signature: #> #> Sig1 Sig2 #> 1 0 2 #> 2 8 0 #> => Assigning a group to a signature with the maxium fraction (stored in 'map_table' attr)... #> [36mℹ[39m [2020-10-09 00:03:40]: Summarizing... #> group #1: 2 samples with Sig2 enriched. #> group #2: 8 samples with Sig1 enriched. #> [33m![39m [2020-10-09 00:03:40]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary). #> [36mℹ[39m [2020-10-09 00:03:40]: 0.043 secs elapsed. grp_label <- grp$group names(grp_label) <- grp$sample
- For COSMIC signatures, the absolute exposure is the estimated mutation counts.
- For copy number signatures, the absolute exposure is the estimated copy number segments.
8.3 Consensus Map
This can only support the result from
sig_extract() with multiple runs.
8.4 Catalogue Profile
Based on plot method for signature, we can plot raw catalogue profile.
At default, the function sums all samples. Users can specify sample ID.