Package: epivizrChart 1.35.0

Hector Corrada Bravo

epivizrChart: R interface to epiviz web components

This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.

Authors:Brian Gottfried [aut], Jayaram Kancherla [aut], Hector Corrada Bravo [aut, cre]

epivizrChart_1.35.0.tar.gz
epivizrChart_1.35.0.zip(r-4.7-any)epivizrChart_1.35.0.zip(r-4.6-any)epivizrChart_1.35.0.zip(r-4.5-any)
epivizrChart_1.35.0.tgz(r-4.6-any)epivizrChart_1.35.0.tgz(r-4.5-any)
epivizrChart_1.35.0.tar.gz(r-4.7-any)epivizrChart_1.35.0.tar.gz(r-4.6-any)
epivizrChart_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epivizrChart/json (API)

# Install 'epivizrChart' in R:
install.packages('epivizrChart', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • bcode_eset - Example expression data from the Gene Expression barcode project
  • cgi_gr - Locations of CpG Islands
  • sumexp - Example SummarizedExperiment for epivizr vignette
  • tcga_colon_blocks - Example methylation data (blocks) for epivizr vignette.
  • tcga_colon_curves - Example methylation data (smoothed methylation levels) for epivizr vignette
  • tcga_colon_expression - Example exon-level RNAseq data from TCGA project for epivizr vignette.

On BioConductor:epivizrChart-1.35.0(bioc 3.24)epivizrChart-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualizationgui

3.15 score 14 scripts 668 downloads 1 mentions 15 exports 88 dependencies

Last updated from:2846232244. Checks:9 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR272
linux-develERROR605
source / vignettesERROR527
linux-releaseERROR603
macos-releaseERROR376
macos-oldrelERROR226
windows-develERROR313
windows-releaseERROR305
windows-oldrelERROR417
wasm-releaseOK281

Exports:append_regionBlocksTrackepivizChartepivizEnvepivizNavHeatmapPlotjson_parserjson_writerLinePlotLineTrackplotScatterPlotStackedBlocksTrackStackedLinePlotStackedLineTrack

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydigestensembldbepivizrDataepivizrServerfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhtmltoolshttpuvhttrIRangesjsonliteKEGGRESTlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganismDbiotelpkgconfigpngpromisesProtGenericsR6RBGLRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Construct URL for Websocket connection between R and UI.constructURL
Initialize Epiviz Chart based on chart type.initialize_chart
(taken from epivizr) register epiviz actions.register_all_the_epiviz_things
(taken from epivizr) print settings in a readable format.settings_as_df
Generic method to add navigation regionsappend_region append_region,EpivizEnvironment-method
Example expression data from the Gene Expression barcode projectbcode_eset
Method to add Blocks TrackBlocksTrack BlocksTrack,EpivizEnvironment-method
Locations of CpG Islandscgi_gr
Get default chart settings and colorschart_default_settings_colors
Data container for an Epiviz Blocks Track.EpivizBlocksTrack EpivizBlocksTrack-class
Initialize an 'EpivizChart' object to visualize in viewer or knit to HTML.epivizChart
Data container for an Epiviz chart component.EpivizChart EpivizChart-class
Class providing data manager for epiviz charts.EpivizChartDataMgr EpivizChartDataMgr-class
Data container for an Epiviz Data Source component.EpivizDataSource EpivizDataSource-class
Initialize an 'EpivizEnvironment' object.epivizEnv
Data container for an Epiviz environment component.EpivizEnvironment EpivizEnvironment-class
Data container for an Epiviz Genes Track.EpivizGenesTrack EpivizGenesTrack-class
Data container for an Epiviz Heatmap Plot.EpivizHeatmapPlot EpivizHeatmapPlot-class
Data container for an Epiviz Genes Track.EpivizIGVTrack EpivizIGVTrack-class
Data container for an Epiviz Line Plot.EpivizLinePlot EpivizLinePlot-class
Data container for an Epiviz Line Track.EpivizLineTrack EpivizLineTrack-class
Initialize an 'EpivizNavigation' object to visualize in viewer or knit to HTML.epivizNav
Data container for an Epiviz navigation component.EpivizNavigation EpivizNavigation-class
Data container for an Epiviz Scatter Plot.EpivizScatterPlot EpivizScatterPlot-class
Data container for an Epiviz Blocks Track.EpivizStackedBlocksTrack EpivizStackedBlocksTrack-class
Data container for an Epiviz Stacked Line Plot.EpivizStackedLinePlot EpivizStackedLinePlot-class
Data container for an Epiviz Stacked Line Track.EpivizStackedLineTrack EpivizStackedLineTrack-class
Data container for an Epiviz web component.EpivizViewComponent EpivizViewComponent-class
Data container for an Epiviz Web component.EpivizWebComponent EpivizWebComponent-class
Construct URL for Websocket connection between R and UIget_available_chart_types
Construct URL for Websocket connection between R and UIget_registered_data_types
Method to add Heatmap PlotHeatmapPlot HeatmapPlot,EpivizEnvironment-method
JSON parser used by this packagejson_parser
JSON writer used by this packagejson_writer
Method to add Line PlotLinePlot LinePlot,EpivizEnvironment-method
Method to add Line TrackLineTrack LineTrack,EpivizEnvironment-method
Generic methods to plot charts and add navigation regionsplot,EpivizEnvironment,ANY-method
Random ID generator for epiviz chartsrand_id
Method to add Scatter PlotScatterPlot ScatterPlot,EpivizEnvironment-method
Method to add Stacked Blocks TrackStackedBlocksTrack StackedBlocksTrack,EpivizEnvironment-method
Method to add Stacked Line PlotStackedLinePlot StackedLinePlot,EpivizEnvironment-method
Method to add Stacked Line TrackStackedLineTrack StackedLineTrack,EpivizEnvironment-method
Example SummarizedExperiment for epivizr vignettesumexp
Example methylation data (blocks) for epivizr vignette.tcga_colon_blocks
Example methylation data (smoothed methylation levels) for epivizr vignettetcga_colon_curves
Example exon-level RNAseq data from TCGA project for epivizr vignette.tcga_colon_expression