生信代码：mutation signature

library(deconstructSigs)
#查看数据
head(sample.mut.ref)
# Convert to deconstructSigs input
sigs.input <- mut.to.sigs.input(mut.ref = sample.mut.ref,
                              sample.id = "Sample",
                              chr = "chr",
                              pos = "pos",
                              ref = "ref",
                              alt = "alt")

# Determine the signatures contributing to the example sample1
sample_1 = whichSignatures(tumor.ref = sigs.input,
                         signatures.ref = signatures.cosmic,
                         sample.id = 1,
                         contexts.needed = TRUE,
                         tri.counts.method = 'default')

#输出tumor的三碱基序列百分比
sample_1$tumor

library(barplot3d)
# Read in COSMIC signature probabilities
x=system.file("extdata", "signature_probabilities.txt", package = "barplot3d")
sigdata=read.table(x,header=TRUE,stringsAsFactors = FALSE)
# 输入文件的顺序必须与此一致
cat(sigdata$Somatic_mutation_type,sep="\n")

#使用自己的数据绘制乐高图
legoplot3d(contextdata=sample_1$tumor,labels=FALSE,scalexy=0.03)

#参数调整
legoplot3d(contextdata=sample_1$tumor,labels=FALSE,scalexy=0.01,sixcolors="broad",alpha=0.4)