Issues

• Are you moving away from supporting plotly integration?

  YuLab-SMU/ggtree#712 · Filter by author lauren-stevens-9 opened on Sep 28, 2026

• geom_cladelab shows up in all panels when using geom_facet

  YuLab-SMU/ggtree#711 · Filter by author eam12 opened on Aug 21, 2026

• Error: object ‘is_ggplot’ is not exported by 'namespace:ggplot2' Execution halted

  YuLab-SMU/ggtree#704 · Filter by author JianzhouJiang opened on Mar 7, 2026
  1

• issue in posterior probability mapping

  YuLab-SMU/ggtree#702 · Filter by author sujigeo opened on Jan 31, 2026
  1

• Can you fix the layout_dendrogram() issue, the scale is reversed

  YuLab-SMU/ggtree#689 · Filter by author xieduo7 opened on Dec 5, 2025

• how to adjust position of geom_tippoint on a tree with equal_angle layout?

  YuLab-SMU/ggtree#687 · Filter by author jayoung opened on Dec 3, 2025
  2

• facet_widths not setting facet widths

  YuLab-SMU/ggtree#685 · Filter by author js-wur opened on Nov 28, 2025

• geom_strip breaks with aes(linetype)

  YuLab-SMU/ggtree#676 · Filter by author joelnitta opened on Oct 29, 2025
  3

• Issue with Rooting S4 Object Using ggtree/treeio Packages

  YuLab-SMU/ggtree#659 · Filter by author Victory-Hugo opened on Jul 10, 2025

• xlim for tree + boxplot => error

  YuLab-SMU/ggtree#658 · Filter by author nick-youngblut opened on Jul 3, 2025
  2

• groupOTU or groupClade

  YuLab-SMU/ggtree#654 · Filter by author sabihayousuf opened on Jun 16, 2025

• ggtree conflict between viewClade,scale_y_reverse, rotate

  YuLab-SMU/ggtree#652 · Filter by author yoelii opened on May 6, 2025

• README missing installation instructions

  YuLab-SMU/ggtree#650 · Filter by author joelnitta opened on Apr 21, 2025

• For some trees, the geome_tiplab angle in "fan" layout may be a little wrong

  YuLab-SMU/ggtree#649 · Filter by author Asa12138 opened on Apr 16, 2025

• geom_rootedge does not allow for no branch lengths if input tree is treedata

  YuLab-SMU/ggtree#648 · Filter by author emilyvansyoc opened on Apr 9, 2025

• geom_tiplab angle off when collapsing clades in circular layout

  YuLab-SMU/ggtree#647 · Filter by author sarahfrail opened on Mar 12, 2025

• Rerooting create polytomy at root where none exists.

  YuLab-SMU/ggtree#644 · Filter by author Tannervanorden opened on Mar 2, 2025

• Specifying tree height and width

  YuLab-SMU/ggtree#643 · Filter by author drdna opened on Feb 1, 2025
  2

• Feature request: extend short branches with dotted lines to make topology visible

  YuLab-SMU/ggtree#640 · Filter by author taprs opened on Nov 26, 2024

• Is it possible to use ggtree to add a columnar stacked bar chart beneath a circular phylogenetic tree?

  YuLab-SMU/ggtree#639 · Filter by author ShanfenO opened on Nov 6, 2024
  1

• geom_tiplab2() is broken with custom coord_polar() settings

  YuLab-SMU/ggtree#638 · Filter by author willgearty opened on Oct 24, 2024
  4

• Independent adjustment of picture and line transparency when using PhyloPic/Images and align=true parameter

  YuLab-SMU/ggtree#633 · Filter by author ilypopv opened on Oct 11, 2024
  1

• Is it possible to add spaces or separation between the squares using gheatmap?

  YuLab-SMU/ggtree#632 · Filter by author kevinlopezreyes opened on Sep 25, 2024

• How to move x axis in heatmap by geom_fruit to top?

  YuLab-SMU/ggtree#630 · Filter by author SilentGene opened on Sep 13, 2024
  1

• "gradient" in geom_hilight does not work properly with coord_flip() or layout_dendrogram()

  YuLab-SMU/ggtree#628 · Filter by author PandengWang opened on Sep 12, 2024