PanVizGenerator: Generate PanViz visualisations from your pangenome
Version 1.4.0

PanViz is a JavaScript based visualisation tool for functionaly annotated pangenomes. PanVizGenerator is a companion for PanViz that facilitates the necessary data preprocessing step necessary to create a working PanViz visualization. The output is fully self-contained so the recipient of the visualization does not need R or PanVizGenerator installed.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Lin Pedersen
Bioconductor views ComparativeGenomics GUI Visualization
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>= 2)
Version1.4.0
URL https://github.com/thomasp85/PanVizGenerator
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PanVizGenerator")

Man pages

getGO: Download and store the Gene Ontology
panviz: Convert pangenome into PanViz
PanVizGenerator: Launch the PanVizGenerator shiny app

Functions

PanVizGenerator Man page Source code
availableTerms Source code
cacheGO Source code
checkTerms Source code
checkVersion Source code
consolidateFiles Source code
copyPanVizFiles Source code
createCluster Source code
createGO Source code
createGeneInfo Source code
createPanData Source code
createPangenome Source code
createScatter Source code
denToList Source code
formatAnnot Source code
formatData Source code
formatEC Source code
formatGO Source code
formatNode Source code
getGO Man page Source code
goToGraph Source code
graphToGo Source code
hasGO Source code
loadGO Source code
oboVersion Source code
onAttach Source code
panviz Man page
panviz,character-method Man page
panviz,data.frame-method Man page
panviz,matrix-method Man page
panviz,pgVirtual-method Man page
parseOBO Source code
pruneGO Source code
server Source code
setDomain Source code
stripEmpty Source code

Files

.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R
R/GO.R
R/IO.R
R/aaa.R
R/panviz.R
R/shinyStuff.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/PanViz
inst/PanViz/PanViz.html
inst/PanViz/README
inst/PanViz/script.js
inst/PanViz/style.css
inst/doc
inst/doc/panviz_howto.R
inst/doc/panviz_howto.Rmd
inst/doc/panviz_howto.html
inst/extdata
inst/extdata/exampleData.csv
inst/server.R
inst/shinyapps
inst/shinyapps/thomas
inst/www
inst/www/code
inst/www/code/scripts.js
inst/www/index.html
inst/www/media
inst/www/media/GitHubLogo.svg
inst/www/media/PanVizLogo1.svg
inst/www/media/PanVizLogo2.svg
inst/www/media/bugs.svg
inst/www/media/goNav1.png
inst/www/media/goNav2.png
inst/www/media/goNav3.png
inst/www/media/panvizDyn1.png
inst/www/media/panvizDyn2.png
inst/www/media/panvizDyn3.png
inst/www/media/share.svg
inst/www/media/strainCom1.png
inst/www/media/strainCom2.png
inst/www/media/visQuery1.png
inst/www/media/visQuery2.png
inst/www/media/visQuery3.png
inst/www/media/visQuery4.png
inst/www/style
inst/www/style/styles.css
man
man/PanVizGenerator.Rd
man/getGO.Rd
man/panviz.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-GO.R
tests/testthat/test-io.R
tests/testthat/test-panviz.R
vignettes
vignettes/panviz_howto.Rmd
vignettes/panvizgenerator.png
PanVizGenerator documentation built on May 20, 2017, 9:33 p.m.