phykit 2.1.67__tar.gz → 2.1.69__tar.gz

{phykit-2.1.67 → phykit-2.1.69}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.67
+Version: 2.1.69
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.67 → phykit-2.1.69}/phykit/cli_registry.py

@@ -97,6 +97,9 @@ ALIAS_TO_HANDLER: Dict[str, str] = {
     "pgls": "phylogenetic_regression",
     "phylo_glm": "phylogenetic_glm",
     "pglm": "phylogenetic_glm",
+    "phylo_logistic": "phylo_logistic",
+    "phylo_logreg": "phylo_logistic",
+    "plogreg": "phylo_logistic",
     "parsimony": "parsimony_score",
     "pars": "parsimony_score",
     "charmap": "character_map",

{phykit-2.1.67 → phykit-2.1.69}/phykit/phykit.py

@@ -237,6 +237,8 @@ class Phykit:
                     - fit phylogenetic generalized least squares (PGLS) regression
                 phylogenetic_glm (alias: phylo_glm; pglm)
                     - fit phylogenetic GLM for binary (logistic) or count (Poisson) data
+                phylo_logistic (alias: phylo_logreg; plogreg)
+                    - fit phylogenetic logistic regression (Ives & Garland 2010)
                 stochastic_character_map (alias: simmap; scm)
                     - stochastic character mapping (SIMMAP) of discrete traits
                 cont_map (alias: contmap; cmap)
@@ -2431,6 +2433,16 @@ class Phykit:
                                             and branch colors (iTOL-
                                             inspired TSV format)
 
+                --plot-ci                   draw confidence interval bars
+                                            at internal nodes on the
+                                            contMap plot (requires --ci
+                                            and --plot)
+
+                --ci-size                   scale factor for CI bar
+                                            size (default: 1.0; use
+                                            2.0 for larger, 0.5 for
+                                            smaller)
+
                 --json                      output results as JSON
                 """
             ),
@@ -2464,6 +2476,14 @@ class Phykit:
             "--plot", type=str, required=False, default=None,
             help=SUPPRESS, metavar=""
         )
+        parser.add_argument(
+            "--plot-ci", action="store_true", required=False, default=False,
+            help=SUPPRESS,
+        )
+        parser.add_argument(
+            "--ci-size", type=float, required=False, default=1.0,
+            help=SUPPRESS, metavar=""
+        )
         add_plot_arguments(parser)
         _add_json_argument(parser)
         _run_service(parser, argv, AncestralReconstruction)
@@ -4269,6 +4289,84 @@ class Phykit:
         _add_json_argument(parser)
         _run_service(parser, argv, PhylogeneticGLM)
 
+    @staticmethod
+    def phylo_logistic(argv):
+        parser = _new_parser(
+            description=textwrap.dedent(
+                f"""\
+                {help_header}
+
+                Fit a Phylogenetic Logistic Regression for binary (0/1)
+                response data while accounting for phylogenetic
+                non-independence among species (Ives & Garland 2010).
+
+                Uses Maximum Penalized Likelihood Estimation (logistic_MPLE)
+                with Firth's bias-correction penalty and jointly estimates
+                the phylogenetic signal parameter alpha via the
+                OU-transformed variance-covariance matrix.
+
+                Input is a phylogenetic tree and a tab-delimited multi-trait
+                file with a header row:
+                taxon<tab>trait1<tab>trait2<tab>...
+
+                Output includes coefficient estimates, standard errors,
+                z-values, p-values, alpha, log-likelihood, penalized
+                log-likelihood, and AIC.
+
+                Aliases:
+                  phylo_logistic, phylo_logreg, plogreg
+                Command line interfaces:
+                  pk_phylo_logistic, pk_phylo_logreg, pk_plogreg
+
+                Usage:
+                phykit phylo_logistic -t <tree> -d <trait_data> --response <column> --predictor <column> [--method logistic_MPLE|logistic_IG10] [--json]
+
+                Options
+                =====================================================
+                -t/--tree                   a tree file
+
+                -d/--trait-data             tab-delimited multi-trait file
+                                            with header row
+
+                --response                  binary response column name
+                                            (must contain only 0 and 1)
+
+                --predictor                 predictor column name(s),
+                                            comma-separated for multiple
+
+                --method                    estimation method: logistic_MPLE
+                                            or logistic_IG10
+                                            (default: logistic_MPLE)
+
+                --json                      optional argument to output
+                                            results as JSON
+                """
+            ),
+        )
+        parser.add_argument(
+            "-t", "--tree", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "-d", "--trait-data", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "--response", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "--predictor", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "--method",
+            type=str,
+            required=False,
+            default="logistic_MPLE",
+            choices=["logistic_MPLE", "logistic_IG10"],
+            help=SUPPRESS,
+            metavar="",
+        )
+        _add_json_argument(parser)
+        _run_service(parser, argv, PhyloLogistic)
+
     @staticmethod
     def stochastic_character_map(argv):
         parser = _new_parser(
@@ -8174,6 +8272,10 @@ def phylogenetic_glm(argv=None):
     Phykit.phylogenetic_glm(sys.argv[1:])
 
 
+def phylo_logistic(argv=None):
+    Phykit.phylo_logistic(sys.argv[1:])
+
+
 def stochastic_character_map(argv=None):
     Phykit.stochastic_character_map(sys.argv[1:])
 

{phykit-2.1.67 → phykit-2.1.69}/phykit/service_factories.py

@@ -71,6 +71,7 @@ PhylogeneticOrdination = _LazyServiceFactory("phykit.services.tree.phylogenetic_
 Phylomorphospace = _LazyServiceFactory("phykit.services.tree.phylomorphospace", "Phylomorphospace")
 PhylogeneticRegression = _LazyServiceFactory("phykit.services.tree.phylogenetic_regression", "PhylogeneticRegression")
 PhylogeneticGLM = _LazyServiceFactory("phykit.services.tree.phylogenetic_glm", "PhylogeneticGLM")
+PhyloLogistic = _LazyServiceFactory("phykit.services.tree.phylo_logistic", "PhyloLogistic")
 StochasticCharacterMap = _LazyServiceFactory("phykit.services.tree.stochastic_character_map", "StochasticCharacterMap")
 ContMap = _LazyServiceFactory("phykit.services.tree.cont_map", "ContMap")
 DensityMap = _LazyServiceFactory("phykit.services.tree.density_map", "DensityMap")

{phykit-2.1.67 → phykit-2.1.69}/phykit/services/tree/__init__.py

@@ -48,6 +48,7 @@ _EXPORTS = {
     "ThresholdModel": "threshold_model",
     "TreenessOverRCV": "treeness_over_rcv",
     "ConcordanceAsr": "concordance_asr",
+    "PhyloLogistic": "phylo_logistic",
     "TraitCorrelation": "trait_correlation",
     "TraitRateMap": "trait_rate_map",
     "TreeSpace": "tree_space",

{phykit-2.1.67 → phykit-2.1.69}/phykit/services/tree/ancestral_reconstruction.py

@@ -48,6 +48,8 @@ class AncestralReconstruction(Tree):
         self.json_output = parsed["json_output"]
         self.trait_type = parsed["trait_type"]
         self.model = parsed["model"]
+        self.plot_ci = parsed["plot_ci"]
+        self.ci_size = parsed["ci_size"]
         self.plot_config = parsed["plot_config"]
 
     def run(self) -> None:
@@ -112,9 +114,11 @@ class AncestralReconstruction(Tree):
         )
 
         if self.plot_output:
+            ci_data = node_cis if (self.plot_ci and self.ci and node_cis) else None
             self._plot_contmap(
                 tree_copy, node_estimates, node_labels,
-                trait_values, trait_name, self.plot_output
+                trait_values, trait_name, self.plot_output,
+                node_cis=ci_data,
             )
             result["plot_output"] = self.plot_output
 
@@ -144,6 +148,8 @@ class AncestralReconstruction(Tree):
             json_output=getattr(args, "json", False),
             trait_type=getattr(args, "type", "continuous"),
             model=getattr(args, "model", "ER"),
+            plot_ci=getattr(args, "plot_ci", False),
+            ci_size=getattr(args, "ci_size", 1.0),
             plot_config=PlotConfig.from_args(args),
         )
 
@@ -809,7 +815,7 @@ class AncestralReconstruction(Tree):
 
     def _plot_contmap(
         self, tree, node_estimates, node_labels, trait_values,
-        trait_name, output_path,
+        trait_name, output_path, node_cis=None,
     ) -> None:
         try:
             import matplotlib
@@ -827,6 +833,7 @@ class AncestralReconstruction(Tree):
 
         # Build estimates dict keyed by id(clade) for all nodes
         all_estimates = {}
+        node_labels_map = {}  # id(clade) → label string (for CI lookup)
         for clade in tree.find_clades(order="preorder"):
             if clade.is_terminal():
                 if clade.name in trait_values:
@@ -834,6 +841,7 @@ class AncestralReconstruction(Tree):
             else:
                 if id(clade) in node_labels:
                     label = node_labels[id(clade)]
+                    node_labels_map[id(clade)] = label
                     if label in node_estimates:
                         all_estimates[id(clade)] = node_estimates[label]
 
@@ -1043,6 +1051,59 @@ class AncestralReconstruction(Tree):
                     fontsize=config.title_fontsize,
                 )
 
+        # Draw CI bars at internal nodes if requested
+        if node_cis:
+            ci_scale = self.ci_size
+            # Build label→id mapping for looking up CI values
+            label_to_id = {}
+            for clade in tree.find_clades(order="preorder"):
+                if not clade.is_terminal() and id(clade) in node_labels_map:
+                    label_to_id[node_labels_map[id(clade)]] = id(clade)
+
+            if config.circular:
+                # Circular: use data coordinates from coords dict
+                for label, (ci_lo, ci_hi) in node_cis.items():
+                    cid = label_to_id.get(label)
+                    if cid is None or cid not in coords:
+                        continue
+                    cx = coords[cid]["x"]
+                    cy = coords[cid]["y"]
+                    angle = coords[cid]["angle"]
+                    # CI bar perpendicular to the radius (tangential)
+                    bar_len = (ci_hi - ci_lo) * ci_scale * 0.3
+                    dx = -np.sin(angle) * bar_len / 2
+                    dy = np.cos(angle) * bar_len / 2
+                    # Main bar
+                    ax.plot([cx - dx, cx + dx], [cy - dy, cy + dy],
+                            color="black", lw=1.5 * ci_scale, zorder=8)
+                    # Point estimate dot
+                    ax.scatter(cx, cy, s=15 * ci_scale, c="black", zorder=9)
+            else:
+                # Rectangular: vertical bars at node positions
+                max_x_val = max(node_x.values()) if node_x else 1.0
+                for label, (ci_lo, ci_hi) in node_cis.items():
+                    cid = label_to_id.get(label)
+                    if cid is None or cid not in node_x or cid not in node_y:
+                        continue
+                    cx = node_x[cid]
+                    cy = node_y[cid]
+                    est = all_estimates.get(cid, (ci_lo + ci_hi) / 2)
+                    # Scale CI width relative to y-axis range
+                    bar_half = (ci_hi - ci_lo) / (vmax - vmin) * 0.4 * ci_scale if vmax != vmin else 0.2 * ci_scale
+                    cap_width = max_x_val * 0.008 * ci_scale
+                    # Vertical bar
+                    ax.plot([cx, cx], [cy - bar_half, cy + bar_half],
+                            color="black", lw=1.2 * ci_scale, zorder=8)
+                    # Caps
+                    ax.plot([cx - cap_width, cx + cap_width],
+                            [cy - bar_half, cy - bar_half],
+                            color="black", lw=1.0 * ci_scale, zorder=8)
+                    ax.plot([cx - cap_width, cx + cap_width],
+                            [cy + bar_half, cy + bar_half],
+                            color="black", lw=1.0 * ci_scale, zorder=8)
+                    # Point estimate dot
+                    ax.scatter(cx, cy, s=12 * ci_scale, c="black", zorder=9)
+
         fig.tight_layout()
         fig.savefig(output_path, dpi=config.dpi, bbox_inches="tight")
         plt.close(fig)