Package: epivizrChart 1.29.0

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_1.29.0.tar.gz
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epivizrChart.pdf |epivizrChart.html✨
epivizrChart/json (API)
NEWS

# Install 'epivizrChart' in R:
install.packages('epivizrChart', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.29.0(bioc 3.21)epivizrChart-1.28.0(bioc 3.20)

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

visualizationgui

3.08 score 12 scripts 205 downloads 1 mentions 15 exports 109 dependencies

Last updated 23 days agofrom:08a69568f3. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 31 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERROROct 31 2024
R-4.3-macERROROct 31 2024

Exports:append_regionBlocksTrackepivizChartepivizEnvepivizNavHeatmapPlotjson_parserjson_writerLinePlotLineTrackplotScatterPlotStackedBlocksTrackStackedLinePlotStackedLineTrack

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrensembldbepivizrDataepivizrServerfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhmshtmltoolshttpuvhttrhttr2IRangesjsonliteKEGGRESTlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganismDbipillarpkgconfigplogrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRBGLRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc

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