Package: CancerEvolutionVisualization 3.0.0

Paul Boutros

CancerEvolutionVisualization: Publication Quality Phylogenetic Tree Plots

Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.

Authors:Paul Boutros [cre], Adriana Salcedo [aut], Dan Knight [aut], Helena Winata [aut], Selina Wu [ctb]

CancerEvolutionVisualization_3.0.0.tar.gz
CancerEvolutionVisualization_3.0.0.zip(r-4.7)CancerEvolutionVisualization_3.0.0.zip(r-4.6)CancerEvolutionVisualization_3.0.0.zip(r-4.5)
CancerEvolutionVisualization_3.0.0.tgz(r-4.6-any)CancerEvolutionVisualization_3.0.0.tgz(r-4.5-any)
CancerEvolutionVisualization_3.0.0.tar.gz(r-4.7-any)CancerEvolutionVisualization_3.0.0.tar.gz(r-4.6-any)
CancerEvolutionVisualization_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CancerEvolutionVisualization/json (API)

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

Bug tracker:https://github.com/uclahs-cds/package-cancerevolutionvisualization/issues

Datasets:
  • colours - Colour scheme vector
  • GRCh37 - GRCh37 Chromosom Information
  • GRCh38 - GRCh38 Chromosom Information
  • snv - SNV dataframe

On CRAN:

Conda:

5.98 score 2 stars 6 scripts 209 downloads 10 exports 22 dependencies

Last updated from:ab3359fdd5. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR195
source / vignettesOK214
linux-release-x86_64ERROR194
macos-release-arm64ERROR112
macos-oldrel-arm64ERROR84
windows-develERROR105
windows-releaseERROR97
windows-oldrelERROR97
wasm-releaseOK125

Exports:create.ccf.densityplotcreate.ccf.heatmapcreate.ccf.summary.heatmapcreate.clone.genome.distribution.plotcreate.cluster.heatmapcreate.phylogenetic.treedata.frame.to.arrayget.colours.in.orderSRCGrobupdate.descendant.property

Dependencies:BoutrosLab.plotting.generalclasscliclusterdeldire1071gluegridExtragtablehexbininterpjpeglatticelatticeExtralifecycleMASSpngproxyRColorBrewerRcppRcppEigenrlang

Reproducing Manuscript Figures
Introduction | Figure 1: Multi-sample Analysis | 1B. CCF Heatmap | 1C. CCF Summary Heatmap | 1D. Clone Genome Distribution Plot | 1G. Multi-sample Phylogenetic Tree | 1G. Single-sample Phylogenetic Tree | Figure 2: Phylogenetic tree features | 2A. Sample-specific subclones | 2B. Annotated single-sample phylogenetic tree | 2C. Mutation timeline tree | 2D. Radial mode with 2 edges | 2E. Dendrogram mode with 2 edges | 2F. Mixed mode with 2 edges | 2G. 500 node phylogentic tree
Rendered fromManuscriptFigures.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2024-12-10

CEV User Guide
Introduction | Installation | CRAN (recommended) | GitHub | Basic Phylogenetic Tree Visualization | Input Phylogenetic Data | Simple Example | Ex. 1.1: Minimal Tree | Ex. 1.2: Using node.id, parent and label columns | Ex. 1.3: Branch Lengths | Ex. 1.4: Branch Scaling | Ex. 1.5: Y-Axis Labels | Ex. 1.6: Axis Tick Placement | Ex. 1.7: Scale Bars | Ex. 1.8: Visualizing Cellular Prevalence | Customizing Node Arrangement | Ex. 2.1: Node Spread | Ex. 2.2: Node Angles | Phylogenetic Tree Modes | Ex. 3.1: Radial Mode | Ex. 3.2: Dendrogram Mode | Customizing Phylogenetic Tree Aesthetics | Supported Aesthetic Input Columns | Line Types | Ex. 4.1: Styled Tree | Ex. 4.2: Nodeless Tree | Text Annotations | Ex. 5.1: Edge annotations | Ex. 5.2: Specifying Text Colour and Style | Additional Plot Parameters | Ex. 6.1: Adding the Normal Node | Ex. 6.2: Horizontal Padding Between Tree and Axes | Ex. 6.3: Plot Title | Ex. 6.4: Saving Plot to file | CCF Distribution Visualization | Input SNV-to-subclone Assignment Data | Ex. 7.1: CCF Distribution Heatmap | Ex. 7.2: CCF Distribution Across subclones | Ex. 7.3: Summary of CCF Distribution | Ex. 7.4: Clone-Genome Distribution Plot
Rendered fromUserGuide.Rmdusingknitr::rmarkdown

Last update: 2024-12-16
Started: 2022-08-02