Package: clevRvis 1.7.0

Sarah Sandmann

clevRvis: Visualization Techniques for Clonal Evolution

clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.

Authors:Sarah Sandmann [aut, cre]

clevRvis_1.7.0.tar.gz
clevRvis_1.7.0.zip(r-4.5)clevRvis_1.7.0.zip(r-4.4)clevRvis_1.7.0.zip(r-4.3)
clevRvis_1.7.0.tgz(r-4.4-any)clevRvis_1.7.0.tgz(r-4.3-any)
clevRvis_1.7.0.tar.gz(r-4.5-noble)clevRvis_1.7.0.tar.gz(r-4.4-noble)
clevRvis_1.7.0.tgz(r-4.4-emscripten)clevRvis_1.7.0.tgz(r-4.3-emscripten)
clevRvis.pdf |clevRvis.html✨
clevRvis/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sandmanns/clevrvis/issues

On BioConductor:clevRvis-1.7.0(bioc 3.21)clevRvis-1.6.0(bioc 3.20)

softwareshinyappsvisualization

4.85 score 7 stars 2 scripts 145 downloads 33 exports 111 dependencies

Last updated 2 months agofrom:6e1b6986d4. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:clevRvisShinycloneFamilycloneFamily<-cloneLabelscloneLabels<-colcol<-combinedPlotcreateSeaObjectdefaultLabelsdefaultLabels<-dolphinPlotexploreTreesextSharkPlotfracTablefracTable<-nestLevelsnestLevels<-originTimepointoriginTimepoint<-parentsparents<-plaicePlotsharkPlotshowtimepointstimepoints<-xposxpos<-ybtmybtm<-ytopytop<-

Dependencies:base64encbitbit64bslibcachemcellrangerclicliprcolorspacecolourpickercommonmarkcowplotcpp11crayoncrosstalkdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggforceggiraphggnewscaleggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoisemgcvmimeminiUImunsellnlmepatchworkpillarpkgconfigpolyclipprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrematchrlangrmarkdownsassscalesshinyshinycssloadersshinydashboardshinyhelpershinyjsshinyWidgetssourcetoolsstringistringrsystemfontstibbletidygraphtidyrtidyselecttinytextweenrtzdbutf8uuidvctrsviridisviridisLitevroomwithrxfunxtableyaml

clevRvis Vignette

Rendered fromclevRvis.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2023-01-04
Started: 2022-11-26

Readme and manuals

Help Manual

Help pageTopics
Visualization Techniques for Clonal EvolutionclevRvis clevRvis_package
A user interface to perform all analyses with clevRvis.clevRvisShiny
Generate a combined basic graph and detailed visualization of clonal evolutioncombinedPlot
Create a seaObjectcreateSeaObject
Generate a detailed visualization of clonal evolutiondolphinPlot
Explore alternative treesexploreTrees
Generate an extended graph visualization of clonal evolutionextSharkPlot
Generate an allele-aware visualization of clonal evolutionplaicePlot
Class seaObjectcloneFamily cloneFamily,seaObject-method cloneFamily<- cloneFamily<-,seaObject-method cloneLabels cloneLabels,seaObject-method cloneLabels<- cloneLabels<-,seaObject-method col col,seaObject-method col<- col<-,seaObject-method defaultLabels defaultLabels,seaObject-method defaultLabels<- defaultLabels<-,seaObject-method fracTable fracTable,seaObject-method fracTable<- fracTable<-,seaObject-method nestLevels nestLevels,seaObject-method nestLevels<- nestLevels<-,seaObject-method originTimepoint originTimepoint,seaObject-method originTimepoint<- originTimepoint<-,seaObject-method parents parents,seaObject-method parents<- parents<-,seaObject-method seaObject-class show show,seaObject-method timepoints timepoints,seaObject-method timepoints<- timepoints<-,seaObject-method xpos xpos,seaObject-method xpos<- xpos<-,seaObject-method ybtm ybtm,seaObject-method ybtm<- ybtm<-,seaObject-method ytop ytop,seaObject-method ytop<- ytop<-,seaObject-method
Generate a basic graph visualization of clonal evolutionsharkPlot