├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── data.R ├── g3Lollipop.R ├── g3LollipopOptions.R ├── g3LollipopTheme.R ├── getMutationsFromCbioportal.R ├── globalVariables.R ├── guessMAFColumn.R ├── hgnc2pfam.R ├── hgnc2uniprot.R ├── mapMutationTypeToMutationClass.R ├── parseProteinChange.R ├── proteinDomain.R ├── readMAF.R ├── uniprot2pfam.R └── zzz.R ├── README.md ├── data-raw ├── TCGA.BRCA.varscan.somatic.maf.gz └── ccle.csv ├── data ├── hgnc2pfam.df.rda └── mutation.table.df.rda ├── docs ├── chart_themes.html └── index.html ├── g3viz.Rproj ├── inst ├── extdata │ ├── TCGA.BRCA.varscan.somatic.maf.gz │ └── ccle.csv └── htmlwidgets │ ├── g3Lollipop.js │ ├── g3Lollipop.yaml │ ├── htmlwidgets.js │ └── lib │ ├── d3 │ └── d3.v4.min.js │ └── g3viz │ ├── g3-lollipop.js │ ├── g3-lollipop.min.css │ └── g3-lollipop.min.js ├── man ├── g3Lollipop-shiny.Rd ├── g3Lollipop.Rd ├── g3Lollipop.options.Rd ├── g3Lollipop.theme.Rd ├── getMutationsFromCbioportal.Rd ├── guessMAFColumnName.Rd ├── hgnc2pfam.Rd ├── hgnc2pfam.df.Rd ├── hgnc2uniprot.Rd ├── mapMutationTypeToMutationClass.Rd ├── mutation.table.df.Rd ├── parseProteinChange.Rd ├── readMAF.Rd └── uniprot2pfam.Rd ├── prepare_data ├── 9606.tsv.gz ├── generate_hgnc2pfam.R └── uniprotkb_taxonomy_id_9606_AND_reviewed_2024_07_29.tsv.gz ├── vignettes ├── .gitignore ├── chart_themes.Rmd ├── figures │ └── color_scheme.png ├── introduction.Rmd └── tables │ ├── chart_options.tsv │ ├── mutation_mapping.tsv │ └── tp53-msk_impact_2017.tsv └── visual_test ├── .gitignore ├── check-themes.R ├── figure_1.log ├── figure_1.pdf ├── figures ├── blue.png ├── cbioportal.png ├── dark.png ├── default.png ├── ggplot2.png ├── nature.png ├── nature2.png ├── simple.png ├── suppl_fig1.png ├── suppl_fig2.png └── suppl_fig3.png ├── graph_example.R ├── suppl_chart_themes.Rmd ├── suppl_chart_themes.pdf ├── suppl_introduction.Rmd ├── suppl_introduction.log ├── suppl_introduction.pdf ├── suppl_table_1.docx ├── suppl_table_1.log ├── suppl_table_1.tex └── tables ├── chart_options.tsv ├── mutation_mapping.tsv └── tp53-msk_impact_2017.tsv /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/G3viz/g3viz/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/G3viz/g3viz/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/G3viz/g3viz/HEAD/.travis.yml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 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