Introduction | Requirements | Installation | Running clevRvis | Examplary use of clevRvis | createSeaObject() | Usage | Details | Time point interpolation | Therapy effect estimation | Examples | sharkPlot() | extSharkPlot() | dolphinPlot() | combinedPlot() | plaicePlot() | exploreTrees() | clevRvisShiny() | Input - without parental relations | Input - with parental relations | (opt.) Explore parental relations | Subsequent analyses | Data | Session information
Package: clevRvis 1.13.0
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:
clevRvis_1.13.0.tar.gz
clevRvis_1.13.0.zip(r-4.7)clevRvis_1.13.0.zip(r-4.6)clevRvis_1.13.0.zip(r-4.5)
clevRvis_1.13.0.tgz(r-4.6-any)clevRvis_1.13.0.tgz(r-4.5-any)
clevRvis_1.13.0.tar.gz(r-4.7-any)clevRvis_1.13.0.tar.gz(r-4.6-any)
clevRvis_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clevRvis/json (API)
| # Install 'clevRvis' in R: |
| install.packages('clevRvis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sandmanns/clevrvis/issues
On BioConductor:clevRvis-1.13.0(bioc 3.24)clevRvis-1.12.0(bioc 3.23)
softwareshinyappsvisualization
Last updated from:f1f60a0e6a. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 187 | ||
| linux-devel-x86_64 | NOTE | 208 | ||
| source / vignettes | OK | 193 | ||
| linux-release-x86_64 | NOTE | 210 | ||
| macos-release-arm64 | NOTE | 103 | ||
| macos-oldrel-arm64 | NOTE | 108 | ||
| windows-devel | NOTE | 129 | ||
| windows-release | NOTE | 139 | ||
| windows-oldrel | NOTE | 132 | ||
| wasm-release | OK | 182 |
Exports:clevRvisShinycloneFamilycloneFamily<-cloneLabelscloneLabels<-colcol<-combinedPlotcreateSeaObjectdefaultLabelsdefaultLabels<-dolphinPlotexploreTreesextSharkPlotfracTablefracTable<-nestLevelsnestLevels<-originTimepointoriginTimepoint<-parentsparents<-plaicePlotsharkPlotshowtimepointstimepoints<-xposxpos<-ybtmybtm<-ytopytop<-
Dependencies:base64encbitbit64bslibcachemcellrangerclicliprcolorspacecolourpickercommonmarkcowplotcpp11crayoncrosstalkdigestdplyrDTevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggiraphggnewscaleggplot2ggraphggrepelgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelitedownmagrittrmarkdownMASSMatrixmemoisemimeminiUIotelpatchworkpillarpkgconfigpolyclipprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrreadxlrematchrlangrmarkdownS7sassscalesshinyshinycssloadersshinydashboardshinyhelpershinyjsshinyWidgetssourcetoolsstringistringrsystemfontstibbletidygraphtidyrtidyselecttinytextweenrtzdbutf8vctrsviridisviridisLitevroomwithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Visualization Techniques for Clonal Evolution | clevRvis clevRvis_package |
| A user interface to perform all analyses with clevRvis. | clevRvisShiny |
| Generate a combined basic graph and detailed visualization of clonal evolution | combinedPlot |
| Create a seaObject | createSeaObject |
| Generate a detailed visualization of clonal evolution | dolphinPlot |
| Explore alternative trees | exploreTrees |
| Generate an extended graph visualization of clonal evolution | extSharkPlot |
| Generate an allele-aware visualization of clonal evolution | plaicePlot |
| Class seaObject | cloneFamily 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 evolution | sharkPlot |
