Package: epivizrChart 1.34.0

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_1.34.0.tar.gz
epivizrChart_1.34.0.zip(r-4.7-any)epivizrChart_1.34.0.zip(r-4.6-any)epivizrChart_1.34.0.zip(r-4.5-any)
epivizrChart_1.34.0.tgz(r-4.6-any)epivizrChart_1.34.0.tgz(r-4.5-any)
epivizrChart_1.34.0.tar.gz(r-4.7-any)epivizrChart_1.34.0.tar.gz(r-4.6-any)
epivizrChart_1.34.0.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-release.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.

visualization gui

4.75 score 14 scripts 526 downloads 1 mentions 15 exports 87 dependencies

Last updated from:ce2ee1e124 (on RELEASE_3_23). Checks:8 ERROR, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	401
linux-devel	ERROR	622
source / vignettes	OK	444
linux-release	ERROR	588
macos-release	ERROR	383
macos-oldrel	ERROR	256
windows-devel	ERROR	361
windows-release	ERROR	431
windows-oldrel	ERROR	414
wasm-release	OK	347

Exports:append_region BlocksTrack epivizChart epivizEnv epivizNav HeatmapPlot json_parser json_writer LinePlot LineTrack plot ScatterPlot StackedBlocksTrack StackedLinePlot StackedLineTrack

Dependencies:abind AnnotationDbi AnnotationFilter askpass base64enc BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray digest ensembldb epivizrData epivizrServer fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue graph htmltools httpuv httr IRanges jsonlite KEGGREST lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl OrganismDbi otel pkgconfig png promises ProtGenerics R6 RBGL Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML XVector yaml

Visualizing Files with epivizrChart

Rendered fromIntegrationWithIGVjs.Rmdusingknitr::rmarkdown

Last update: 2018-10-09
Started: 2018-05-17

Visualizing genomic data in Shiny Apps using epivizrChart

Rendered fromIntegrationWithShiny.Rmdusingknitr::rmarkdown

Last update: 2018-08-24
Started: 2018-05-17

Visualizing Epiviz Web Components with epivizrChart

Rendered fromIntroToEpivizrChart.Rmdusingknitr::rmarkdown

Last update: 2018-07-15
Started: 2017-07-24

Visualizing RangeSummarizedExperiment objects Shiny Apps using epivizrChart

Rendered fromVisualizeSumExp.Rmdusingknitr::rmarkdown

Last update: 2018-07-15
Started: 2018-05-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 regions	append_region append_region,EpivizEnvironment-method
Example expression data from the Gene Expression barcode project	bcode_eset
Method to add Blocks Track	BlocksTrack BlocksTrack,EpivizEnvironment-method
Locations of CpG Islands	cgi_gr
Get default chart settings and colors	chart_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 UI	get_available_chart_types
Construct URL for Websocket connection between R and UI	get_registered_data_types
Method to add Heatmap Plot	HeatmapPlot HeatmapPlot,EpivizEnvironment-method
JSON parser used by this package	json_parser
JSON writer used by this package	json_writer
Method to add Line Plot	LinePlot LinePlot,EpivizEnvironment-method
Method to add Line Track	LineTrack LineTrack,EpivizEnvironment-method
Generic methods to plot charts and add navigation regions	plot,EpivizEnvironment,ANY-method
Random ID generator for epiviz charts	rand_id
Method to add Scatter Plot	ScatterPlot ScatterPlot,EpivizEnvironment-method
Method to add Stacked Blocks Track	StackedBlocksTrack StackedBlocksTrack,EpivizEnvironment-method
Method to add Stacked Line Plot	StackedLinePlot StackedLinePlot,EpivizEnvironment-method
Method to add Stacked Line Track	StackedLineTrack StackedLineTrack,EpivizEnvironment-method
Example SummarizedExperiment for epivizr vignette	sumexp
Example methylation data (blocks) for epivizr vignette.	tcga_colon_blocks
Example methylation data (smoothed methylation levels) for epivizr vignette	tcga_colon_curves
Example exon-level RNAseq data from TCGA project for epivizr vignette.	tcga_colon_expression