What problem does phylorug solve? | Brief history | Nodal support versus nodal stability | Quick start | Load the data | Check taxon consistency | Build the node presence matrix | Plot the rug | Support mode | Reading the rug plot | Fine-tuning the figure | Working with real data: Culicomorpha | Read the trees | Root and remove the outgroups | Choose a backbone | Build the matrix and plot | Presence mode | What the rug reveals | Full pipeline: beetles with tip translation | Root and drop outgroups | Translate tip labels | Choose a backbone and check taxa | Customisation | Dots in support mode | Universal thresholds (no support_type) | Grid dimensions | Tree appearance | Including the backbone | Custom thresholds | Selecting which nodes to visualize | Tips and best practices | References
Package: phylorug 0.1.0
Md Rifath Ahamed
phylorug: Visualize Clade Recovery and Support Across Phylogenetic Trees
Generates rug plot visualizations directly on tree nodes to illustrate clade recovery and support from multiple phylogenetic and phylogenomic analyses. As modern studies routinely employ diverse datasets and inference techniques producing potentially conflicting trees, 'phylorug' simplifies the comparison among these trees by consolidating clade recovery and support on a reference tree.
Authors:
phylorug_0.1.0.tar.gz
phylorug_0.1.0.zip(r-4.7-any)phylorug_0.1.0.zip(r-4.6-any)
phylorug_0.1.0.tar.gz(r-4.7-any)phylorug_0.1.0.tar.gz(r-4.6-any)
phylorug_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylorug/json (API)
| # Install 'phylorug' in R: |
| install.packages('phylorug', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mdrifathahamed/phylorug/issues
Pkgdown/docs site:https://mdrifathahamed.github.io
Datasets:
- sample_trees - Sample beetle phylogenies
Last updated from:cbfe1c4c71. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 156 | ||
| source / vignettes | OK | 201 | ||
| linux-release | OK | 114 | ||
| windows-devel | OK | 63 | ||
| windows-release | OK | 82 | ||
| wasm-release | OK | 117 |
Exports:add_treecheck_taxanode_presence_matrixplot_phylorugprune_to_sharedread_treestranslate_tips
Dependencies:apeclicpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogRcpprlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add a comparison tree to an existing node presence matrix | add_tree |
| Diagnose taxon consistency between backbone and comparison trees | check_taxa |
| Tabulate clade recovery and support across trees | node_presence_matrix |
| Draw a phylorug: a backbone tree with rug plots on every internal node | plot_phylorug |
| Trim the backbone and its comparison trees to their shared set of taxa | prune_to_shared |
| Import phylogenetic trees from a directory | read_trees |
| Sample beetle phylogenies (15-taxon subset) | sample_trees |
| Relabel tips across a list of trees using a lookup table | translate_tips |