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-4.5)CancerEvolutionVisualization_3.0.0.zip(r-4.4)CancerEvolutionVisualization_3.0.0.zip(r-4.3)
CancerEvolutionVisualization_3.0.0.tgz(r-4.4-any)CancerEvolutionVisualization_3.0.0.tgz(r-4.3-any)
CancerEvolutionVisualization_3.0.0.tar.gz(r-4.5-noble)CancerEvolutionVisualization_3.0.0.tar.gz(r-4.4-noble)
CancerEvolutionVisualization_3.0.0.tgz(r-4.4-emscripten)CancerEvolutionVisualization_3.0.0.tgz(r-4.3-emscripten)
CancerEvolutionVisualization.pdf |CancerEvolutionVisualization.html✨
CancerEvolutionVisualization/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

6.18 score 2 stars 5 scripts 188 downloads 8 exports 22 dependencies

Last updated 25 days agofrom:95ddb597b1. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 07 2025
R-4.5-winNOTEJan 07 2025
R-4.5-linuxNOTEJan 07 2025
R-4.4-winNOTEJan 07 2025
R-4.4-macNOTEJan 07 2025
R-4.3-winNOTEJan 07 2025
R-4.3-macNOTEJan 07 2025

Exports:create.ccf.heatmapcreate.ccf.summary.heatmapcreate.clone.genome.distribution.plotcreate.cluster.heatmapcreate.phylogenetic.treedata.frame.to.arraySRCGrobupdate.descendant.property

Dependencies:BoutrosLab.plotting.generalclasscliclusterdeldire1071gluegridExtragtablehexbininterpjpeglatticelatticeExtralifecycleMASSpngproxyRColorBrewerRcppRcppEigenrlang

Reproducing Manuscript Figures

Helena Winata

Rendered fromManuscriptFigures.Rmdusingrmarkdownon Jan 07 2025.

Last update: 2024-12-16
Started: 2024-12-10

CEV User Guide

Dan Knight, Helena Winata

Rendered fromUserGuide.Rmdusingknitr::rmarkdownon Jan 07 2025.

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

Readme and manuals

Help Manual

Help pageTopics
Colour scheme vectorcolours
CCF Distribution Heatmapcreate.ccf.heatmap
CCF Summary Heatmapcreate.ccf.summary.heatmap
Create Clone Genome Distribution Plotcreate.clone.genome.distribution.plot
Cluster Heatmapcreate.cluster.heatmap
Phylogenetic Tree Plotcreate.phylogenetic.tree
Convert Data Frame to Arraydata.frame.to.array
GRCh37 Chromosom InformationGRCh37
GRCh38 Chromosom InformationGRCh38
SNV dataframesnv
Subclone Tree PlotSRCGrob
Update Tree Descendant Propertyupdate.descendant.property