# 1. 数据获取 —— 改为 LAML（急性髓系白血病）
LAML_maf <- TCGAmutations::tcga_load(study = "LAML")
LAML_maf # 查看 MAF 对象摘要
getFields(LAML_maf) # 显示字段
getSampleSummary(LAML_maf) # 样本总结
getGeneSummary(LAML_maf) # 基因突变频率
clinicalData <- getClinicalData(LAML_maf) # 获取临床信息
# 2. 绘制突变概览图
plotmafSummary(maf = LAML_maf, rmOutlier = TRUE, addStat = "median", dashboard = TRUE, titvRaw = FALSE)
# 3. 瀑布图（Oncoplot）—— 显示前15个高频突变基因
oncoplot(maf = LAML_maf, top = 15, borderCol = NULL, fontSize = 0.8)
oncoplot(maf = LAML_maf, genes = c("FLT3", "NPM1", "CEBPA"), borderCol = NULL) # AML 常见驱动基因
# 4. 结合临床信息绘图（示例：病理分期或风险等级）
oncoplot(maf = LAML_maf, top = 15, sortByAnnotation = TRUE, clinicalFeatures = 'FAB_classification')
oncoplot(maf = LAML_maf, top = 15, clinicalFeatures = 'cytogenetic_risk')
oncoplot(maf = LAML_maf, top = 15, sortByAnnotation = TRUE,
annotationOrder = c("Poor", "Intermediate", "Favorable"),
clinicalFeatures = 'cytogenetic_risk', borderCol = NULL)
# 5. 通路水平 oncoplot（若包支持）
oncoplot(maf = LAML_maf, pathways = "smgbp", gene_mar = 12, fontSize = 0.7,
sortByAnnotation = TRUE, clinicalFeatures = 'cytogenetic_risk', borderCol = NULL)
# 6. 单个基因分析（例如 FLT3，常见于 AML）
plotProtein(gene = "FLT3", refSeqID = "NM_004119")
lollipopPlot(maf = LAML_maf, gene = 'FLT3', AACol = 'HGVSp_Short',
refSeqID = "NM_004119", showMutationRate = TRUE)
# 7. 生存分析（OS 和 PFI）
maftools::mafSurvival(maf = LAML_maf, genes = c("FLT3"), time = "OS.time", Status = "OS")
maftools::mafSurvival(maf = LAML_maf, genes = c("NPM1"), time = "PFI.time", Status = "PFI")
# 8. 突变互斥性与共现性分析
somaticInteractions(maf = LAML_maf, top = 15, pvalue = c(0.05, 0.01))
根据代码按照上述文件写论文
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博客介绍了maftools这一MAF文件可视化工具，可用于对MAF文件进行可视化操作，在信息技术领域有助于相关数据的直观呈现与分析。
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