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seqcombo 1.35.1

  • fix link aesthetic mappings (l_width/l_alpha) being ignored with elbow links, and stagger shared elbow positions automatically so their vertical segments no longer overlap
  • spread viruses sharing the same coordinate into evenly spaced slots via set_layout(..., spread = TRUE) (enabled by default in layout_timeline()), carry metadata columns (including facet variables) into link and label layers, and duplicate flows that cross facets so they remain visible in each panel
  • refine vignette examples that suffered from stacked viruses and overlapping links
  • add a curated host color palette: seqcombo_host_palette(), apply_seqcombo_palette() for label-to-color mapping, and scale_seqcombo_host() as ready-made colour/fill scales
  • extend example_seqcombo_data() with long and genotype teaching datasets, alongside the existing basic and timeline variants
  • improve ggplot2 compatibility by replacing deprecated aes_() usage and switching line border sizing to linewidth
  • add validation for flow_info ids and empty segment_color entries, and preserve existing coordinates for nodes not present in flow_info
  • add build_virus_info() and build_flow_info() helpers, set_layout(..., preserve_x / preserve_y), and curved reassortment links
  • add build_flow_info_from_long(), segment labels inside virus glyphs, and build_segment_caption() for figure annotations
  • add link aesthetics mapped from flow_info, a dedicated layout_timeline() helper, and faceting support via facet_by
  • add seqcombo_data convenience helpers, autoplot(), check_seqcombo_data(), example_seqcombo_data(), and theme_seqcombo_pub() for publication-style workflows
  • refresh package metadata, including the package title, description, and BugReports URL, and add the rlang import
  • migrate the package vignette from .Rmd to Quarto .qmd and update the vignette build workflow
  • standardize historical NEWS.md entries and fix typos for older releases
  • replace the legacy docs/-based GitHub Pages flow with deployment from a dedicated gh-pages branch via GitHub Actions
  • remove deploy.sh and seqcombo.Rproj
  • remove legacy artifacts, including the outdated/ examples folder, the retired .travis.yml config, and unreferenced vignette screenshots

seqcombo 1.34.0

  • Bioconductor RELEASE_3_23 (2026-04-29, Wed)

seqcombo 1.32.0

  • Bioconductor RELEASE_3_22 (2025-11-01, Sat)

seqcombo 1.30.0

  • Bioconductor RELEASE_3_21 (2025-04-17, Thu)

seqcombo 1.28.0

  • Bioconductor RELEASE_3_20 (2024-10-30, Wed)

seqcombo 1.26.0

  • Bioconductor RELEASE_3_19 (2024-05-15, Wed)

seqcombo 1.24.0

  • Bioconductor RELEASE_3_18 (2023-10-25, Wed)

seqcombo 1.18.0

  • Bioconductor RELEASE_3_16 (2022-11-02, Wed)

seqcombo 1.17.1

  • update docs (2021-12-15, Wed)
  • remove code that was incorporated into ggmsa

seqcombo 1.16.0

  • Bioconductor RELEASE_3_14

seqcombo 1.15.1

  • import yulab.utils (2021-08-20, Fri)
  • move seqdiff and simplot to the ggmsa package

seqcombo 1.14.0

  • Bioconductor RELEASE_3_13

seqcombo 1.12.0

  • Bioconductor RELEASE_3_12 (2020-10-28, Wed)

seqcombo 1.5.1

  • fix R CMD check by importing dplyr::n (2019-01-02, Wed)

seqcombo 1.1.1

  • better simplot implementation (2018-01-09, Fri)

seqcombo 0.99.11

  • add geom_genotype (2017-08-29, Tue)

seqcombo 0.99.10

  • add geom_hybrid (2017-08-17, Thu)

seqcombo 0.99.9

  • add hybrid_plot (2017-06-30, Fri)

seqcombo 0.0.3

  • add more parameters for plot, by, xlab, color, and fill

seqcombo 0.0.2

  • add vignette

seqcombo 0.0.1

  • initial version with a plot method for nucleotide differences between two aligned sequences (2016-11-16, Wed)