phykit 2.1.50__tar.gz → 2.1.51__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (123) hide show
  1. {phykit-2.1.50 → phykit-2.1.51}/PKG-INFO +1 -1
  2. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/plot_config.py +30 -0
  3. {phykit-2.1.50 → phykit-2.1.51}/phykit/phykit.py +141 -29
  4. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/ancestral_reconstruction.py +23 -17
  5. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/character_map.py +4 -21
  6. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/concordance_asr.py +12 -9
  7. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/cont_map.py +12 -9
  8. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/cophylo.py +12 -9
  9. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/density_map.py +12 -9
  10. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/discordance_asymmetry.py +12 -9
  11. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylo_heatmap.py +11 -8
  12. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/quartet_pie.py +11 -8
  13. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/rate_heterogeneity.py +11 -8
  14. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/stochastic_character_map.py +12 -9
  15. phykit-2.1.51/phykit/version.py +1 -0
  16. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/PKG-INFO +1 -1
  17. phykit-2.1.50/phykit/version.py +0 -1
  18. {phykit-2.1.50 → phykit-2.1.51}/LICENSE.md +0 -0
  19. {phykit-2.1.50 → phykit-2.1.51}/README.md +0 -0
  20. {phykit-2.1.50 → phykit-2.1.51}/phykit/__init__.py +0 -0
  21. {phykit-2.1.50 → phykit-2.1.51}/phykit/__main__.py +0 -0
  22. {phykit-2.1.50 → phykit-2.1.51}/phykit/cli_registry.py +0 -0
  23. {phykit-2.1.50 → phykit-2.1.51}/phykit/errors.py +0 -0
  24. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/__init__.py +0 -0
  25. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/boolean_argument_parsing.py +0 -0
  26. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/caching.py +0 -0
  27. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/discrete_models.py +0 -0
  28. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/files.py +0 -0
  29. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/json_output.py +0 -0
  30. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/parallel.py +0 -0
  31. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/parsimony_utils.py +0 -0
  32. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/quartet_utils.py +0 -0
  33. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/stats_summary.py +0 -0
  34. {phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/streaming.py +0 -0
  35. {phykit-2.1.50 → phykit-2.1.51}/phykit/service_factories.py +0 -0
  36. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/__init__.py +0 -0
  37. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/__init__.py +0 -0
  38. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/alignment_entropy.py +0 -0
  39. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/alignment_length.py +0 -0
  40. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/alignment_length_no_gaps.py +0 -0
  41. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/alignment_outlier_taxa.py +0 -0
  42. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/alignment_recoding.py +0 -0
  43. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/base.py +0 -0
  44. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/column_score.py +0 -0
  45. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/composition_per_taxon.py +0 -0
  46. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/compositional_bias_per_site.py +0 -0
  47. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/create_concatenation_matrix.py +0 -0
  48. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/dna_threader.py +0 -0
  49. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/evolutionary_rate_per_site.py +0 -0
  50. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/faidx.py +0 -0
  51. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/gc_content.py +0 -0
  52. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/mask_alignment.py +0 -0
  53. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/occupancy_per_taxon.py +0 -0
  54. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/pairwise_identity.py +0 -0
  55. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/parsimony_informative_sites.py +0 -0
  56. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/plot_alignment_qc.py +0 -0
  57. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/rcv.py +0 -0
  58. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/rcvt.py +0 -0
  59. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/rename_fasta_entries.py +0 -0
  60. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/sum_of_pairs_score.py +0 -0
  61. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/alignment/variable_sites.py +0 -0
  62. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/base.py +0 -0
  63. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/__init__.py +0 -0
  64. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/base.py +0 -0
  65. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/bipartition_support_stats.py +0 -0
  66. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/branch_length_multiplier.py +0 -0
  67. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/collapse_branches.py +0 -0
  68. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/consensus_network.py +0 -0
  69. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/consensus_tree.py +0 -0
  70. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/covarying_evolutionary_rates.py +0 -0
  71. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/dvmc.py +0 -0
  72. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/evo_tempo_map.py +0 -0
  73. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/evolutionary_rate.py +0 -0
  74. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/fit_continuous.py +0 -0
  75. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/fit_discrete.py +0 -0
  76. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/hidden_paralogy_check.py +0 -0
  77. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/independent_contrasts.py +0 -0
  78. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/internal_branch_stats.py +0 -0
  79. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/internode_labeler.py +0 -0
  80. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/kf_distance.py +0 -0
  81. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/last_common_ancestor_subtree.py +0 -0
  82. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/lb_score.py +0 -0
  83. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/ltt.py +0 -0
  84. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/monophyly_check.py +0 -0
  85. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/nearest_neighbor_interchange.py +0 -0
  86. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/network_signal.py +0 -0
  87. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/ou_shift_detection.py +0 -0
  88. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/ouwie.py +0 -0
  89. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/parsimony_score.py +0 -0
  90. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/patristic_distances.py +0 -0
  91. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phenogram.py +0 -0
  92. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylogenetic_glm.py +0 -0
  93. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylogenetic_ordination.py +0 -0
  94. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylogenetic_regression.py +0 -0
  95. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylogenetic_signal.py +0 -0
  96. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/phylomorphospace.py +0 -0
  97. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/polytomy_test.py +0 -0
  98. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/print_tree.py +0 -0
  99. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/prune_tree.py +0 -0
  100. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/quartet_network.py +0 -0
  101. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/relative_rate_test.py +0 -0
  102. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/rename_tree_tips.py +0 -0
  103. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/rf_distance.py +0 -0
  104. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/root_tree.py +0 -0
  105. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/saturation.py +0 -0
  106. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/spectral_discordance.py +0 -0
  107. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/spurious_sequence.py +0 -0
  108. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/terminal_branch_stats.py +0 -0
  109. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/threshold_model.py +0 -0
  110. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/tip_labels.py +0 -0
  111. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/tip_to_tip_distance.py +0 -0
  112. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/tip_to_tip_node_distance.py +0 -0
  113. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/total_tree_length.py +0 -0
  114. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/treeness.py +0 -0
  115. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/treeness_over_rcv.py +0 -0
  116. {phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/vcv_utils.py +0 -0
  117. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/SOURCES.txt +0 -0
  118. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/dependency_links.txt +0 -0
  119. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/entry_points.txt +0 -0
  120. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/requires.txt +0 -0
  121. {phykit-2.1.50 → phykit-2.1.51}/phykit.egg-info/top_level.txt +0 -0
  122. {phykit-2.1.50 → phykit-2.1.51}/setup.cfg +0 -0
  123. {phykit-2.1.50 → phykit-2.1.51}/setup.py +0 -0
{phykit-2.1.50 → phykit-2.1.51}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phykit
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- Version: 2.1.50
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+ Version: 2.1.51
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  Home-page: https://github.com/jlsteenwyk/phykit
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  Author: Jacob L. Steenwyk
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  Author-email: jlsteenwyk@gmail.com
{phykit-2.1.50 → phykit-2.1.51}/phykit/helpers/plot_config.py RENAMED
@@ -24,6 +24,7 @@ class PlotConfig:
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  axis_fontsize: Optional[float] = None
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  colors: Optional[List[str]] = None
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  ladderize: bool = False
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+ cladogram: bool = False
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  def validate(self) -> None:
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  if self.fig_width is not None and self.fig_width <= 0:
@@ -189,6 +190,7 @@ class PlotConfig:
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  axis_fontsize=getattr(args, "axis_fontsize", None),
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  colors=colors,
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  ladderize=getattr(args, "ladderize", False),
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+ cladogram=getattr(args, "cladogram", False),
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  )
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  config.validate()
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  return config
@@ -208,3 +210,31 @@ def add_plot_arguments(parser) -> None:
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  group.add_argument("--axis-fontsize", type=float, default=None, help="Font size for axis labels")
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  group.add_argument("--colors", type=str, default=None, help="Comma-separated colors (hex or named)")
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  group.add_argument("--ladderize", action="store_true", default=False, help="Ladderize (sort) the tree before plotting")
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+ group.add_argument("--cladogram", action="store_true", default=False, help="Draw cladogram (equal branch lengths, tips aligned) instead of phylogram")
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+
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+
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+ def compute_node_x_cladogram(tree, parent_map):
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+ """Compute cladogram x-coordinates: tips aligned at right, internal nodes at depth.
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+
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+ Returns dict mapping node id -> x-coordinate (0.0 to 1.0 range).
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+ """
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+ root = tree.root
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+ node_depth = {}
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+ for clade in tree.find_clades(order="preorder"):
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+ if clade == root:
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+ node_depth[id(clade)] = 0
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+ elif id(clade) in parent_map:
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+ parent = parent_map[id(clade)]
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+ node_depth[id(clade)] = node_depth.get(id(parent), 0) + 1
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+
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+ max_depth = max(node_depth.values()) if node_depth else 1
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+ step_size = 1.0 / max(max_depth, 1)
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+
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+ node_x = {}
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+ for clade in tree.find_clades(order="preorder"):
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+ cid = id(clade)
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+ if clade.is_terminal():
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+ node_x[cid] = float(max_depth) * step_size
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+ else:
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+ node_x[cid] = float(node_depth.get(cid, 0)) * step_size
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+ return node_x
{phykit-2.1.50 → phykit-2.1.51}/phykit/phykit.py RENAMED
@@ -466,7 +466,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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- [--colors <str>] [--ladderize]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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  Options
@@ -517,6 +517,10 @@ class Phykit:
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  --ladderize ladderize (sort) the tree
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ lengths, tips aligned)
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+ instead of phylogram
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+
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  --json optional argument to output
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  results as JSON
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  """
@@ -821,7 +825,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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@@ -870,6 +874,10 @@ class Phykit:
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  --ladderize ladderize (sort) the tree
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ lengths, tips aligned)
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+ instead of phylogram
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+
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  --json optional argument to output
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  results as JSON
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  """
@@ -955,7 +963,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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  Options
@@ -1003,6 +1011,10 @@ class Phykit:
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  --ladderize ladderize (sort) the tree
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ lengths, tips aligned)
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+ instead of phylogram
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+
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  --json optional argument to output
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  results as JSON
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  """
@@ -1309,7 +1321,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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  Options
@@ -1362,6 +1374,10 @@ class Phykit:
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  --ladderize ladderize (sort) the tree
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ instead of phylogram
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  --json optional argument to output
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  results as JSON
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  """
@@ -1499,7 +1515,7 @@ class Phykit:
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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@@ -1547,6 +1563,10 @@ class Phykit:
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  --ladderize ladderize (sort) the tree
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ instead of phylogram
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  results as JSON
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  """
@@ -1793,7 +1813,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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  Options
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  =====================================================
@@ -1947,7 +1967,7 @@ class Phykit:
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  [--legend-position <str>]
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  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
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  [--title-fontsize <float>] [--axis-fontsize <float>]
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+ [--colors <str>] [--ladderize] [--cladogram]
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  [--json]
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  Options
@@ -2007,6 +2027,10 @@ class Phykit:
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  before plotting
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+ --cladogram draw cladogram (equal branch
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+ lengths, tips aligned)
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+ instead of phylogram
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  --json output results as JSON
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2035
  """
2012
2036
  ),
@@ -2080,7 +2104,7 @@ class Phykit:
2080
2104
  [--legend-position <str>]
2081
2105
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
2082
2106
  [--title-fontsize <float>] [--axis-fontsize <float>]
2083
- [--colors <str>] [--ladderize]
2107
+ [--colors <str>] [--ladderize] [--cladogram]
2084
2108
  [--json]
2085
2109
 
2086
2110
  Options
@@ -2141,6 +2165,10 @@ class Phykit:
2141
2165
  --ladderize ladderize (sort) the tree
2142
2166
  before plotting
2143
2167
 
2168
+ --cladogram draw cladogram (equal branch
2169
+ lengths, tips aligned)
2170
+ instead of phylogram
2171
+
2144
2172
  --json output results as JSON
2145
2173
  """
2146
2174
  ),
@@ -2371,7 +2399,7 @@ class Phykit:
2371
2399
  [--legend-position <str>]
2372
2400
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
2373
2401
  [--title-fontsize <float>] [--axis-fontsize <float>]
2374
- [--colors <str>] [--ladderize]
2402
+ [--colors <str>] [--ladderize] [--cladogram]
2375
2403
  [--json]
2376
2404
 
2377
2405
  Options
@@ -2432,6 +2460,10 @@ class Phykit:
2432
2460
  --ladderize ladderize (sort) the tree
2433
2461
  before plotting
2434
2462
 
2463
+ --cladogram draw cladogram (equal branch
2464
+ lengths, tips aligned)
2465
+ instead of phylogram
2466
+
2435
2467
  --json optional argument to output
2436
2468
  results as JSON
2437
2469
  """
@@ -3045,7 +3077,7 @@ class Phykit:
3045
3077
  [--legend-position <str>]
3046
3078
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
3047
3079
  [--title-fontsize <float>] [--axis-fontsize <float>]
3048
- [--colors <str>] [--ladderize]
3080
+ [--colors <str>] [--ladderize] [--cladogram]
3049
3081
  [--json]
3050
3082
 
3051
3083
  Options
@@ -3134,6 +3166,10 @@ class Phykit:
3134
3166
  --ladderize ladderize (sort) the tree
3135
3167
  before plotting
3136
3168
 
3169
+ --cladogram draw cladogram (equal branch
3170
+ lengths, tips aligned)
3171
+ instead of phylogram
3172
+
3137
3173
  --json optional argument to output
3138
3174
  results as JSON
3139
3175
  """
@@ -3383,7 +3419,7 @@ class Phykit:
3383
3419
  [--legend-position <str>]
3384
3420
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
3385
3421
  [--title-fontsize <float>] [--axis-fontsize <float>]
3386
- [--colors <str>] [--ladderize]
3422
+ [--colors <str>] [--ladderize] [--cladogram]
3387
3423
  [--json]
3388
3424
 
3389
3425
  Options
@@ -3438,6 +3474,10 @@ class Phykit:
3438
3474
  --ladderize ladderize (sort) the tree
3439
3475
  before plotting
3440
3476
 
3477
+ --cladogram draw cladogram (equal branch
3478
+ lengths, tips aligned)
3479
+ instead of phylogram
3480
+
3441
3481
  --json optional argument to output
3442
3482
  results as JSON
3443
3483
  """
@@ -3737,7 +3777,7 @@ class Phykit:
3737
3777
  [--legend-position <str>]
3738
3778
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
3739
3779
  [--title-fontsize <float>] [--axis-fontsize <float>]
3740
- [--colors <str>] [--ladderize]
3780
+ [--colors <str>] [--ladderize] [--cladogram]
3741
3781
  [--json]
3742
3782
 
3743
3783
  Options
@@ -3795,6 +3835,10 @@ class Phykit:
3795
3835
  --ladderize ladderize (sort) the tree
3796
3836
  before plotting
3797
3837
 
3838
+ --cladogram draw cladogram (equal branch
3839
+ lengths, tips aligned)
3840
+ instead of phylogram
3841
+
3798
3842
  --json optional argument to output
3799
3843
  results as JSON
3800
3844
  """
@@ -3865,7 +3909,7 @@ class Phykit:
3865
3909
  [--legend-position <str>]
3866
3910
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
3867
3911
  [--title-fontsize <float>] [--axis-fontsize <float>]
3868
- [--colors <str>] [--ladderize]
3912
+ [--colors <str>] [--ladderize] [--cladogram]
3869
3913
  [--json]
3870
3914
 
3871
3915
  Options
@@ -3911,6 +3955,10 @@ class Phykit:
3911
3955
  --ladderize ladderize (sort) the tree
3912
3956
  before plotting
3913
3957
 
3958
+ --cladogram draw cladogram (equal branch
3959
+ lengths, tips aligned)
3960
+ instead of phylogram
3961
+
3914
3962
  --json optional argument to also
3915
3963
  output results as JSON
3916
3964
  """
@@ -3960,7 +4008,7 @@ class Phykit:
3960
4008
  [--legend-position <str>]
3961
4009
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
3962
4010
  [--title-fontsize <float>] [--axis-fontsize <float>]
3963
- [--colors <str>] [--ladderize]
4011
+ [--colors <str>] [--ladderize] [--cladogram]
3964
4012
  [--json]
3965
4013
 
3966
4014
  Options
@@ -4016,6 +4064,10 @@ class Phykit:
4016
4064
  --ladderize ladderize (sort) the tree
4017
4065
  before plotting
4018
4066
 
4067
+ --cladogram draw cladogram (equal branch
4068
+ lengths, tips aligned)
4069
+ instead of phylogram
4070
+
4019
4071
  --json optional argument to also
4020
4072
  output results as JSON
4021
4073
  """
@@ -4070,7 +4122,7 @@ class Phykit:
4070
4122
  [--legend-position <str>]
4071
4123
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
4072
4124
  [--title-fontsize <float>] [--axis-fontsize <float>]
4073
- [--colors <str>] [--ladderize]
4125
+ [--colors <str>] [--ladderize] [--cladogram]
4074
4126
  [--json]
4075
4127
 
4076
4128
  Options
@@ -4116,6 +4168,10 @@ class Phykit:
4116
4168
  --ladderize ladderize (sort) the tree
4117
4169
  before plotting
4118
4170
 
4171
+ --cladogram draw cladogram (equal branch
4172
+ lengths, tips aligned)
4173
+ instead of phylogram
4174
+
4119
4175
  --json optional argument to output
4120
4176
  results as JSON
4121
4177
  """
@@ -4162,7 +4218,7 @@ class Phykit:
4162
4218
  [--legend-position <str>]
4163
4219
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
4164
4220
  [--title-fontsize <float>] [--axis-fontsize <float>]
4165
- [--colors <str>] [--ladderize]
4221
+ [--colors <str>] [--ladderize] [--cladogram]
4166
4222
  [--json]
4167
4223
 
4168
4224
  Options
@@ -4211,6 +4267,10 @@ class Phykit:
4211
4267
  --ladderize ladderize (sort) the tree
4212
4268
  before plotting
4213
4269
 
4270
+ --cladogram draw cladogram (equal branch
4271
+ lengths, tips aligned)
4272
+ instead of phylogram
4273
+
4214
4274
  --json optional argument to output
4215
4275
  results as JSON
4216
4276
  """
@@ -4264,7 +4324,7 @@ class Phykit:
4264
4324
  [--legend-position <str>]
4265
4325
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
4266
4326
  [--title-fontsize <float>] [--axis-fontsize <float>]
4267
- [--colors <str>] [--ladderize]
4327
+ [--colors <str>] [--ladderize] [--cladogram]
4268
4328
  [--json]
4269
4329
 
4270
4330
  Options
@@ -4319,6 +4379,10 @@ class Phykit:
4319
4379
  --ladderize ladderize (sort) the tree
4320
4380
  before plotting
4321
4381
 
4382
+ --cladogram draw cladogram (equal branch
4383
+ lengths, tips aligned)
4384
+ instead of phylogram
4385
+
4322
4386
  --json optional argument to output
4323
4387
  results as JSON
4324
4388
  """
@@ -4806,7 +4870,7 @@ class Phykit:
4806
4870
  [--legend-position <str>]
4807
4871
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
4808
4872
  [--title-fontsize <float>] [--axis-fontsize <float>]
4809
- [--colors <str>] [--ladderize]
4873
+ [--colors <str>] [--ladderize] [--cladogram]
4810
4874
  [--json]
4811
4875
 
4812
4876
  Options
@@ -4860,6 +4924,10 @@ class Phykit:
4860
4924
  --ladderize ladderize (sort) the tree
4861
4925
  before plotting
4862
4926
 
4927
+ --cladogram draw cladogram (equal branch
4928
+ lengths, tips aligned)
4929
+ instead of phylogram
4930
+
4863
4931
  --json optional argument to output
4864
4932
  results as JSON
4865
4933
  """
@@ -4924,7 +4992,7 @@ class Phykit:
4924
4992
  [--legend-position <str>]
4925
4993
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
4926
4994
  [--title-fontsize <float>] [--axis-fontsize <float>]
4927
- [--colors <str>] [--ladderize]
4995
+ [--colors <str>] [--ladderize] [--cladogram]
4928
4996
 
4929
4997
  Options
4930
4998
  =====================================================
@@ -4976,6 +5044,10 @@ class Phykit:
4976
5044
  --ladderize ladderize (sort) the tree
4977
5045
  before plotting
4978
5046
 
5047
+ --cladogram draw cladogram (equal branch
5048
+ lengths, tips aligned)
5049
+ instead of phylogram
5050
+
4979
5051
  --json optional argument to output
4980
5052
  per-node concordance as JSON
4981
5053
  """
@@ -5047,7 +5119,7 @@ class Phykit:
5047
5119
  [--legend-position <str>]
5048
5120
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
5049
5121
  [--title-fontsize <float>] [--axis-fontsize <float>]
5050
- [--colors <str>] [--ladderize]
5122
+ [--colors <str>] [--ladderize] [--cladogram]
5051
5123
  [--json]
5052
5124
 
5053
5125
  Options
@@ -5107,6 +5179,10 @@ class Phykit:
5107
5179
  --ladderize ladderize (sort) the tree
5108
5180
  before plotting
5109
5181
 
5182
+ --cladogram draw cladogram (equal branch
5183
+ lengths, tips aligned)
5184
+ instead of phylogram
5185
+
5110
5186
  --json optional argument to output
5111
5187
  results as JSON
5112
5188
  """
@@ -5272,7 +5348,7 @@ class Phykit:
5272
5348
  [--legend-position <str>]
5273
5349
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
5274
5350
  [--title-fontsize <float>] [--axis-fontsize <float>]
5275
- [--colors <str>] [--ladderize]
5351
+ [--colors <str>] [--ladderize] [--cladogram]
5276
5352
  [--json]
5277
5353
 
5278
5354
  Options
@@ -5321,6 +5397,10 @@ class Phykit:
5321
5397
  --ladderize ladderize (sort) the tree
5322
5398
  before plotting
5323
5399
 
5400
+ --cladogram draw cladogram (equal branch
5401
+ lengths, tips aligned)
5402
+ instead of phylogram
5403
+
5324
5404
  --json optional argument to output
5325
5405
  results as JSON
5326
5406
  """
@@ -5429,7 +5509,7 @@ class Phykit:
5429
5509
  [--legend-position <str>]
5430
5510
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
5431
5511
  [--title-fontsize <float>] [--axis-fontsize <float>]
5432
- [--colors <str>] [--ladderize]
5512
+ [--colors <str>] [--ladderize] [--cladogram]
5433
5513
  [--json]
5434
5514
 
5435
5515
  Options
@@ -5480,6 +5560,10 @@ class Phykit:
5480
5560
  --ladderize ladderize (sort) the tree
5481
5561
  before plotting
5482
5562
 
5563
+ --cladogram draw cladogram (equal branch
5564
+ lengths, tips aligned)
5565
+ instead of phylogram
5566
+
5483
5567
  --json optional argument to output
5484
5568
  results as JSON
5485
5569
  """
@@ -5539,7 +5623,7 @@ class Phykit:
5539
5623
  [--legend-position <str>]
5540
5624
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
5541
5625
  [--title-fontsize <float>] [--axis-fontsize <float>]
5542
- [--colors <str>] [--ladderize]
5626
+ [--colors <str>] [--ladderize] [--cladogram]
5543
5627
  [--json]
5544
5628
 
5545
5629
  Options
@@ -5606,6 +5690,10 @@ class Phykit:
5606
5690
  --ladderize ladderize (sort) the tree
5607
5691
  before plotting
5608
5692
 
5693
+ --cladogram draw cladogram (equal branch
5694
+ lengths, tips aligned)
5695
+ instead of phylogram
5696
+
5609
5697
  --json optional argument to output
5610
5698
  results as JSON
5611
5699
  """
@@ -6005,7 +6093,7 @@ class Phykit:
6005
6093
  [--legend-position <str>]
6006
6094
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6007
6095
  [--title-fontsize <float>] [--axis-fontsize <float>]
6008
- [--colors <str>] [--ladderize]
6096
+ [--colors <str>] [--ladderize] [--cladogram]
6009
6097
  [--json]
6010
6098
 
6011
6099
  Options
@@ -6065,6 +6153,10 @@ class Phykit:
6065
6153
  --ladderize ladderize (sort) the tree
6066
6154
  before plotting
6067
6155
 
6156
+ --cladogram draw cladogram (equal branch
6157
+ lengths, tips aligned)
6158
+ instead of phylogram
6159
+
6068
6160
  --json optional argument to output
6069
6161
  results as JSON
6070
6162
  """
@@ -6244,7 +6336,7 @@ class Phykit:
6244
6336
  [--legend-position <str>]
6245
6337
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6246
6338
  [--title-fontsize <float>] [--axis-fontsize <float>]
6247
- [--colors <str>] [--ladderize]
6339
+ [--colors <str>] [--ladderize] [--cladogram]
6248
6340
  [--json]
6249
6341
 
6250
6342
  Options
@@ -6298,6 +6390,10 @@ class Phykit:
6298
6390
  --ladderize ladderize (sort) the tree
6299
6391
  before plotting
6300
6392
 
6393
+ --cladogram draw cladogram (equal branch
6394
+ lengths, tips aligned)
6395
+ instead of phylogram
6396
+
6301
6397
  --json optional argument to output
6302
6398
  results as JSON
6303
6399
  """
@@ -6416,7 +6512,7 @@ class Phykit:
6416
6512
  [--legend-position <str>]
6417
6513
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6418
6514
  [--title-fontsize <float>] [--axis-fontsize <float>]
6419
- [--colors <str>] [--ladderize]
6515
+ [--colors <str>] [--ladderize] [--cladogram]
6420
6516
  [--json]
6421
6517
 
6422
6518
  Options
@@ -6464,6 +6560,10 @@ class Phykit:
6464
6560
  --ladderize ladderize (sort) the tree
6465
6561
  before plotting
6466
6562
 
6563
+ --cladogram draw cladogram (equal branch
6564
+ lengths, tips aligned)
6565
+ instead of phylogram
6566
+
6467
6567
  --json optional argument to output
6468
6568
  results as JSON
6469
6569
  """
@@ -6519,7 +6619,7 @@ class Phykit:
6519
6619
  [--legend-position <str>]
6520
6620
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6521
6621
  [--title-fontsize <float>] [--axis-fontsize <float>]
6522
- [--colors <str>] [--ladderize]
6622
+ [--colors <str>] [--ladderize] [--cladogram]
6523
6623
  [--json]
6524
6624
 
6525
6625
  Options
@@ -6566,6 +6666,10 @@ class Phykit:
6566
6666
  --ladderize ladderize (sort) the tree
6567
6667
  before plotting
6568
6668
 
6669
+ --cladogram draw cladogram (equal branch
6670
+ lengths, tips aligned)
6671
+ instead of phylogram
6672
+
6569
6673
  --json optional argument to output
6570
6674
  results as JSON
6571
6675
  """
@@ -6628,7 +6732,7 @@ class Phykit:
6628
6732
  [--legend-position <str>]
6629
6733
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6630
6734
  [--title-fontsize <float>] [--axis-fontsize <float>]
6631
- [--colors <str>] [--ladderize]
6735
+ [--colors <str>] [--ladderize] [--cladogram]
6632
6736
  [--json]
6633
6737
 
6634
6738
  Options
@@ -6689,6 +6793,10 @@ class Phykit:
6689
6793
  --ladderize ladderize (sort) the tree
6690
6794
  before plotting
6691
6795
 
6796
+ --cladogram draw cladogram (equal branch
6797
+ lengths, tips aligned)
6798
+ instead of phylogram
6799
+
6692
6800
  --json output results as JSON
6693
6801
  """
6694
6802
  ),
@@ -6762,7 +6870,7 @@ class Phykit:
6762
6870
  [--legend-position <str>]
6763
6871
  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
6764
6872
  [--title-fontsize <float>] [--axis-fontsize <float>]
6765
- [--colors <str>] [--ladderize]
6873
+ [--colors <str>] [--ladderize] [--cladogram]
6766
6874
 
6767
6875
  Options
6768
6876
  =====================================================
@@ -6825,6 +6933,10 @@ class Phykit:
6825
6933
  --ladderize ladderize (sort) the tree
6826
6934
  before plotting
6827
6935
 
6936
+ --cladogram draw cladogram (equal branch
6937
+ lengths, tips aligned)
6938
+ instead of phylogram
6939
+
6828
6940
  --json optional argument to output
6829
6941
  results as JSON
6830
6942
  """
{phykit-2.1.50 → phykit-2.1.51}/phykit/services/tree/ancestral_reconstruction.py RENAMED
@@ -9,7 +9,7 @@ from scipy.optimize import minimize
9
9
 
10
10
  from .base import Tree
11
11
  from ...helpers.json_output import print_json
12
- from ...helpers.plot_config import PlotConfig
12
+ from ...helpers.plot_config import PlotConfig, compute_node_x_cladogram
13
13
  from ...helpers.discrete_models import (
14
14
  build_q_matrix,
15
15
  matrix_exp,
@@ -831,14 +831,17 @@ class AncestralReconstruction(Tree):
831
831
 
832
832
  # Assign x-positions via preorder traversal
833
833
  root = tree.root
834
- for clade in tree.find_clades(order="preorder"):
835
- if clade == root:
836
- node_x[id(clade)] = 0.0
837
- else:
838
- if id(clade) in parent_map:
839
- parent = parent_map[id(clade)]
840
- t = clade.branch_length if clade.branch_length else 0.0
841
- node_x[id(clade)] = node_x[id(parent)] + t
834
+ if self.plot_config.cladogram:
835
+ node_x = compute_node_x_cladogram(tree, parent_map)
836
+ else:
837
+ for clade in tree.find_clades(order="preorder"):
838
+ if clade == root:
839
+ node_x[id(clade)] = 0.0
840
+ else:
841
+ if id(clade) in parent_map:
842
+ parent = parent_map[id(clade)]
843
+ t = clade.branch_length if clade.branch_length else 0.0
844
+ node_x[id(clade)] = node_x[id(parent)] + t
842
845
 
843
846
  # Assign internal y-positions (mean of children)
844
847
  for clade in tree.find_clades(order="postorder"):
@@ -1413,14 +1416,17 @@ class AncestralReconstruction(Tree):
1413
1416
 
1414
1417
  # Assign x-positions via preorder traversal
1415
1418
  root = tree.root
1416
- for clade in tree.find_clades(order="preorder"):
1417
- if clade == root:
1418
- node_x[id(clade)] = 0.0
1419
- else:
1420
- if id(clade) in parent_map:
1421
- parent = parent_map[id(clade)]
1422
- t = clade.branch_length if clade.branch_length else 0.0
1423
- node_x[id(clade)] = node_x[id(parent)] + t
1419
+ if self.plot_config.cladogram:
1420
+ node_x = compute_node_x_cladogram(tree, parent_map)
1421
+ else:
1422
+ for clade in tree.find_clades(order="preorder"):
1423
+ if clade == root:
1424
+ node_x[id(clade)] = 0.0
1425
+ else:
1426
+ if id(clade) in parent_map:
1427
+ parent = parent_map[id(clade)]
1428
+ t = clade.branch_length if clade.branch_length else 0.0
1429
+ node_x[id(clade)] = node_x[id(parent)] + t
1424
1430
 
1425
1431
  # Internal y-positions (mean of children)
1426
1432
  for clade in tree.find_clades(order="postorder"):