Codes in paper

Use GenVisR package to draw heat map of driver mutation

Introduction

Use GenVisR package to draw heat map of driver mutation

Code explanation

Load the package, read in the data

Its input data’drivers_lung.txt’ part is as follows

NICKEL SULFATE HEXAHYDRATE 6    7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
SODIUM TUNGSTATE DIHYDRATE 5    7   130177854   C   T   Fgfr2   c.1741G>A   p.V581I Missense_Mutation
SODIUM TUNGSTATE DIHYDRATE 5    7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
VINYLIDENE CHLORIDE 1   7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
VINYLIDENE CHLORIDE 3   7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
NICKEL OXIDE 2  6   145246771   C   T   Kras    c.35G>A p.G12D  Missense_Mutation
ANTIMONY TRIOXIDE 3 6   145246771   C   T   Kras    c.35G>A p.G12D  Missense_Mutation
ANTIMONY TRIOXIDE 3 9   120950606   C   G   Ctnnb1  c.98C>G p.S33C  Missense_Mutation
SODIUM TUNGSTATE DIHYDRATE 4    7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
ANTIMONY TRIOXIDE 4 6   145246772   C   A   Kras    c.34G>T p.G12C  Missense_Mutation
ANTIMONY TRIOXIDE 5 6   145246769   C   G   Kras    c.37G>C p.G13R  Missense_Mutation
ISOBUTYL NITRITE 6  7   130196315   A   G   Fgfr2   c.1201T>C   p.C401R Missense_Mutation
Code show as below
library("GenVisR")

main_layer <- theme_grey()+theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1,size=7,color=1))
custom_pallete <- c("grey30","grey90","steelblue1","yellow","pink","green")
geneslung <- read.delim('drivers_lung.txt',header=F,sep='\t')
colnames(geneslung) <- c('Tumor_Sample_Barcode','chr','pos','ref','alt','Hugo_Symbol','Change','Changep','Variant_Classification')
Here we use the waterfall function of the GenVisR package to draw a mutation waterfall chart. mainLabelCol = "Changep" parameter setting grid displays the amino acid changes inside. mainXlabel=T Add the name label of the x-axis sample. mainPalette=custom_pallete use custom color palette
pdf("Fig-4a.pdf",height=5,width=12)
waterfall(geneslung,mainXlabel=T,main_geneLabSize=12,mainLabelCol = "Changep",mainLabelAngle = 90, mainLabelSize = 2,mainDropMut = TRUE,section_heights = c(0, 1),mainLayer = main_layer,mainPalette=custom_pallete)
dev.off()


Driver genes detected in at least 3% of lung tumors. Kras, Fgfr2 and Braf mutations are mutually exclusive

Interpretation of results

Shows some detected driver mutations

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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