Package: g3viz 1.2.0

Xin Guo

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:Xin Guo [aut, cre], Rener Zhang [ctb], Ruining Zhu [ctb], Feng Zhao [ctb]

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

Datasets:

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

On CRAN:

bioinformatics genomics-visualization lollipop-plot variants visualize-mutation-data

5.56 score 29 stars 21 scripts 388 downloads 3 mentions 13 exports 61 dependencies

Last updated 2 months agofrom:fa6d3d80ed. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 10 2024
R-4.5-win	OK	Oct 10 2024
R-4.5-linux	OK	Oct 10 2024
R-4.4-win	OK	Oct 10 2024
R-4.4-mac	OK	Oct 10 2024
R-4.3-win	OK	Oct 10 2024
R-4.3-mac	OK	Oct 10 2024

Exports:g3Lollipop g3Lollipop.options g3Lollipop.theme g3LollipopOutput getMutationsFromCbioportal guessMAFColumnName hgnc2pfam hgnc2uniprot mapMutationTypeToMutationClass parseProteinChange readMAF renderG3Lollipop uniprot2pfam

Dependencies:AnnotationDbi askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem cli cpp11 crayon curl DBI digest evaluate fastmap fontawesome fs GenomeInfoDb GenomeInfoDbData glue highr htmltools htmlwidgets httr httr2 IRanges jquerylib jsonlite KEGGREST knitr lifecycle magrittr memoise mime openssl org.Hs.eg.db pkgconfig plogr png R6 rappdirs rlang rmarkdown RSQLite S4Vectors sass stringi stringr sys tinytex UCSC.utils vctrs withr xfun XVector yaml zlibbioc

Citation

Development and contributors

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