Mutation MAF summary plot
Mutation Annotation Format (MAF) is a TCGA defined file format, used to store mutation annotation informations.
MAF is a specific file format for human species, it contains SNV and annotation informations for all samples, easily for downstream analysis. You can change VCF file into MAF file with vcf2maf. Here we used Masked Somatic Mutation, open access mutation annotation files. ref: maftool R package.
build-in TCGA 33 types of cancers (TCGA.*.mutect*somatic.maf.gz)
Examples from paper
M 5 C regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in lung adenocarcinoma. Fig2A
select cancer types and input genes
1) How to plot?
1, Prepare data
2, Open with excel, and change into the same format as the example
3, Copy and paste data into the input frame
4, Select parameters
5, Submit and download figure files
2) Why NO figure generated?
Script need strigent input format, please read the instructions and examples carefully.
3) How to cite?
800+ papers cited (Google Scholar). You can cite the original package, or using the following format:
Heatmap was plotted by https://www.bioinformatics.com.cn/en, a free online platform for data analysis and visualization.