使用GenVisR包進行驅動突變的熱圖繪制
介紹
通過熱圖顯示突變的整體情況
代碼講解
加載包，讀入數據
它的輸入數據’drivers_lung.txt’部分如下
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代碼如下
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')這里用GenVisR包的waterfall函數進行突變的瀑布圖繪制.。mainLabelCol = "Changep"參數設置格子顯示里面的氨基酸變化。mainXlabel=T添加x軸樣本名字標簽。mainPalette=custom_pallete使用自定義色板
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
結果解讀
顯示了部分檢測到的driver突變
參考文獻
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
原始文章