Codes in paper

Mutation signature upstream and downstream base bar diagram drawing

Introduction

Show the mutation signal of a sample

Code explanation

Load the package, read in the
library(MutationalPatterns)
nhdp <- readRDS('mousesignatures_norm.rds'

Its input data’nhdp’ part is as follows, each row is the corresponding upstream and downstream clips, and each column is the signal type

> str(nhdp)
 num [1:96, 1:11] 0.01985 0.01188 0.00248 0.01138 0.01724 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:96] "1" "2" "3" "4" ...
  ..$ : chr [1:11] "SBS5" "SBS40" "SBS19" "SBS_N1" ...

The author originally used SigprofilerPlotting for drawing in Python, and later used the plot_96_profile function of the R package MutationalPatterns

#I used SigprofilerPlotting in python, however here I obtain the same results using MutationalPatterns
#for Figure 5b 
#I want to show mSBS19 and some liver samples where I found with SBS19 

signb=cbind(nhdp[,3],humandata[,c('Liver-HCC::SP97771','Liver-HCC::SP112141')])
colnames(signb)=c('mSB19','Liver-HCC:SP97771','Liver-HCC:SP112141')

fig5b<-plot_96_profile(signb,ymax=0.09)

ggsave(plot=fig5b, file='figure-5b.pdf', device=cairo_pdf, width=7, height=5)
main_layer <- theme_grey()+theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1,size=7,color=1))


mSBS19 and two spectra of human hepatocellular carcinomas where SBS19 was identified are shown.

Interpretation of results

Shows SBS19 signals identified in human cancer samples

References

Riva, L., Pandiri, A. R., Li, Y. R., Droop, A., Hewinson, J., Quail, M. A., … Adams, D. J. (2020). The mutational signature profile of known and suspected human carcinogens in mice. Nature Genetics. doi:10.1038/s41588-020-0692-4

Original code

https://github.com/team113sanger/mouse-mutatation-signatures

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