Package: clevRvis 1.5.0

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_1.5.0.tar.gz
clevRvis_1.5.0.zip(r-4.5)clevRvis_1.5.0.zip(r-4.4)clevRvis_1.5.0.zip(r-4.3)
clevRvis_1.5.0.tgz(r-4.4-any)clevRvis_1.5.0.tgz(r-4.3-any)
clevRvis_1.5.0.tar.gz(r-4.5-noble)clevRvis_1.5.0.tar.gz(r-4.4-noble)
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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'))

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

On BioConductor:clevRvis-1.5.0(bioc 3.20)clevRvis-1.4.0(bioc 3.19)

bioconductor-package

33 exports 0.36 score 113 dependencies

Last updated 2 months agofrom:d3649dd251

Exports:clevRvisShiny cloneFamily cloneFamily<-cloneLabels cloneLabels<-col col<-combinedPlot createSeaObject defaultLabels defaultLabels<-dolphinPlot exploreTrees extSharkPlot fracTable fracTable<-nestLevels nestLevels<-originTimepoint originTimepoint<-parents parents<-plaicePlot sharkPlot show timepoints timepoints<-xpos xpos<-ybtm ybtm<-ytop ytop<-

Dependencies:anytime base64enc BH bit bit64 bslib cachem cellranger cli clipr colorspace colourpicker commonmark cowplot cpp11 crayon crosstalk digest dplyr DT evaluate fansi farver fastmap fontawesome fs generics ggforce ggiraph ggnewscale ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable highr hms htmltools htmlwidgets httpuv igraph isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr markdown MASS Matrix memoise mgcv mime miniUI munsell nlme patchwork pillar pkgconfig polyclip prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr readxl rematch rlang rmarkdown sass scales shiny shinycssloaders shinydashboard shinyhelper shinyjs shinyWidgets sourcetools stringi stringr systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr tzdb utf8 uuid vctrs viridis viridisLite vroom withr xfun xtable yaml

clevRvis Vignette

Rendered fromclevRvis.Rmdusingknitr::rmarkdownon Jun 20 2024.

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

Citation

Development and contributors

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