Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R
- 1Shanghai Jiao Tong University
Abstract
Background: Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive configuration, predictable diagnostics, and machine-readable exit status. Results: We present Rclade, an R package that consolidates the multi-package coordination required for taxonomic collapsing into a streamlined, single-function interface. Rclade provides (1) custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that bypass coord_munch() interpolation to achieve straight-edge rendering of collapsed triangles in circular layouts; (2) automatic detection and parsing of four taxonomic-label formats (GTDB, Silva, NCBI, embedded) plus user-supplied custom regex, with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets; and (3) workflow embeddability through YAML configuration, library-mode APIs, and standard Unix exit codes. Benchmarks on synthetic and real datasets (200-10,000 synthetic tips and real reference trees up to 10,122 tips; 5 replicates at every scale under a unified fully rendered measurement protocol) show that the full-pipeline overhead is modest for interactive use (median {approx}0.87 s in-session rendering and {approx}8.4 s process-level wall-clock at 10,000 tips). Conclusions: Rclade is a convenience layer over the ggtree/deeptime ecosystem that reduces boilerplate while adding targeted technical improvements for circular-layout rendering and format heterogeneity management.
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BibTeX
@misc{zeng2026rclade,
title = {{Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R}},
author = {Z. Zeng and Y. Wang},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.27.747462},
url = {https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R
AU - Z. Zeng
AU - Y. Wang
PY - 2026
DA - 2026/08/27
PB - bioRxiv
DO - 10.64898/2026.08.27.747462
UR - https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1
AB - Background: Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive configuration, predictable diagnostics, and machine-readable exit status. Results: We present Rclade, an R package that consolidates the multi-package coordination required for taxonomic collapsing into a streamlined, single-function interface. Rclade provides (1) custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that bypass coord_munch() interpolation to achieve straight-edge rendering of collapsed triangles in circular layouts; (2) automatic detection and parsing of four taxonomic-label formats (GTDB, Silva, NCBI, embedded) plus user-supplied custom regex, with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets; and (3) workflow embeddability through YAML configuration, library-mode APIs, and standard Unix exit codes. Benchmarks on synthetic and real datasets (200-10,000 synthetic tips and real reference trees up to 10,122 tips; 5 replicates at every scale under a unified fully rendered measurement protocol) show that the full-pipeline overhead is modest for interactive use (median {approx}0.87 s in-session rendering and {approx}8.4 s process-level wall-clock at 10,000 tips). Conclusions: Rclade is a convenience layer over the ggtree/deeptime ecosystem that reduces boilerplate while adding targeted technical improvements for circular-layout rendering and format heterogeneity management.
ER -