Package: g3viz 1.2.0
g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram
Interface for 'g3-lollipop' 'JavaScript' library. Visualize genetic mutation data using an interactive lollipop diagram in 'RStudio' or your web browser.
Authors:
g3viz_1.2.0.tar.gz
g3viz_1.2.0.zip(r-4.5)g3viz_1.2.0.zip(r-4.4)g3viz_1.2.0.zip(r-4.3)
g3viz_1.2.0.tgz(r-4.4-any)g3viz_1.2.0.tgz(r-4.3-any)
g3viz_1.2.0.tar.gz(r-4.5-noble)g3viz_1.2.0.tar.gz(r-4.4-noble)
g3viz_1.2.0.tgz(r-4.4-emscripten)g3viz_1.2.0.tgz(r-4.3-emscripten)
g3viz.pdf |g3viz.html✨
g3viz/json (API)
NEWS
# Install 'g3viz' in R: |
install.packages('g3viz', repos = c('https://g3viz.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/g3viz/g3viz/issues
- hgnc2pfam.df - Mapping table between gene.symbol, uniprot.id, and pfam
- mutation.table.df - Default mapping table between mutation type (aka, variant classification) to mutation class
bioinformaticsgenomics-visualizationlollipop-plotvariantsvisualize-mutation-data
Last updated 2 months agofrom:fa6d3d80ed. Checks:OK: 6 WARNING: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 09 2024 |
R-4.5-win | OK | Nov 09 2024 |
R-4.5-linux | WARNING | Nov 09 2024 |
R-4.4-win | OK | Nov 09 2024 |
R-4.4-mac | OK | Nov 09 2024 |
R-4.3-win | OK | Nov 09 2024 |
R-4.3-mac | OK | Nov 09 2024 |
Exports:g3Lollipopg3Lollipop.optionsg3Lollipop.themeg3LollipopOutputgetMutationsFromCbioportalguessMAFColumnNamehgnc2pfamhgnc2uniprotmapMutationTypeToMutationClassparseProteinChangereadMAFrenderG3Lollipopuniprot2pfam
Dependencies:AnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemclicpp11crayoncurlDBIdigestevaluatefastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDatagluehighrhtmltoolshtmlwidgetshttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlifecyclemagrittrmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6rappdirsrlangrmarkdownRSQLiteS4VectorssassstringistringrsystinytexUCSC.utilsvctrswithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Render g3lollipop diagram for the given mutation data | g3Lollipop |
Shiny bindings for g3Lollipop | g3Lollipop-shiny g3LollipopOutput renderG3Lollipop |
G3Lollipop plot options | g3Lollipop.options |
G3Lollipop chart options of built-in themes. | g3Lollipop.theme |
Query cancer genomic mutation data from cBioPortal | getMutationsFromCbioportal |
Guess column name for MAF file | guessMAFColumnName |
Map from Hugo symbol to Pfam domains | hgnc2pfam |
Mapping table between gene.symbol, uniprot.id, and pfam | hgnc2pfam.df |
Mapping from Hugo symbol to UniProt IDs | hgnc2uniprot |
Map from mutation type (aka, variant classification) to mutation class | mapMutationTypeToMutationClass |
Default mapping table between mutation type (aka, variant classification) to mutation class | mutation.table.df |
Extract _amino_acid_position_ from _Protein_Change_ | parseProteinChange |
Read MAF file | readMAF |
From UniProt ID to Pfam-A domain composition | uniprot2pfam |