phykit 2.1.73__tar.gz → 2.1.74__tar.gz

{phykit-2.1.73 → phykit-2.1.74}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.73
+Version: 2.1.74
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.73 → phykit-2.1.74}/phykit/phykit.py

@@ -7598,6 +7598,9 @@ class Phykit:
 
                 -v/--verbose                print per-branch details
 
+                --annotate                  show gCF values on the
+                                            plot near each branch
+
                 --fig-width                 figure width in inches
                                             (auto-scaled if omitted)
 
@@ -7662,6 +7665,10 @@ class Phykit:
         parser.add_argument(
             "-v", "--verbose", action="store_true", required=False, help=SUPPRESS
         )
+        parser.add_argument(
+            "--annotate", action="store_true", required=False, default=False,
+            help=SUPPRESS,
+        )
         add_plot_arguments(parser)
         _add_json_argument(parser)
         _run_service(parser, argv, DiscordanceAsymmetry)

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/ancestral_reconstruction.py

@@ -939,7 +939,9 @@ class AncestralReconstruction(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -1012,11 +1014,13 @@ class AncestralReconstruction(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -1655,7 +1659,9 @@ class AncestralReconstruction(Tree):
                     start_angle += sweep
 
             # Tip labels
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations
             if self.plot_config.color_file:
@@ -1750,12 +1756,14 @@ class AncestralReconstruction(Tree):
             # Tip labels with state color
             max_x_val = max(node_x.values()) if node_x else 0
             offset = max_x_val * 0.02
-            for tip in tips:
-                color = state_colors.get(tip_states.get(tip.name, ""), "black")
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9, color=color,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    color = state_colors.get(tip_states.get(tip.name, ""), "black")
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize, color=color,
+                    )
 
             # Apply color annotations
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/concordance_asr.py

@@ -844,7 +844,9 @@ class ConcordanceAsr(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -915,11 +917,13 @@ class ConcordanceAsr(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/cont_map.py

@@ -522,7 +522,9 @@ class ContMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -592,11 +594,13 @@ class ContMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/density_map.py

@@ -347,7 +347,9 @@ class DensityMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -453,11 +455,13 @@ class DensityMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/discordance_asymmetry.py

@@ -33,6 +33,7 @@ class DiscordanceAsymmetry(Tree):
         super().__init__(tree_file_path=parsed["tree_file_path"])
         self.gene_trees_path = parsed["gene_trees_path"]
         self.verbose = parsed["verbose"]
+        self.annotate = parsed["annotate"]
         self.json_output = parsed["json_output"]
         self.plot_output = parsed["plot_output"]
         self.plot_config = parsed["plot_config"]
@@ -42,6 +43,7 @@ class DiscordanceAsymmetry(Tree):
             tree_file_path=args.tree,
             gene_trees_path=args.gene_trees,
             verbose=getattr(args, "verbose", False),
+            annotate=getattr(args, "annotate", False),
             json_output=getattr(args, "json", False),
             plot_output=getattr(args, "plot_output", None),
             plot_config=PlotConfig.from_args(args),
@@ -314,7 +316,9 @@ class DiscordanceAsymmetry(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, species_tree, coords, fontsize=9, offset=max_x * 0.02)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, species_tree, coords, fontsize=label_fontsize, offset=max_x * 0.02)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -345,23 +349,28 @@ class DiscordanceAsymmetry(Tree):
 
                 total = entry["n_concordant"] + entry["n_alt1"] + entry["n_alt2"]
                 gcf = entry["n_concordant"] / total if total > 0 else 1.0
-                ax.annotate(
-                    f"gCF={gcf:.2f}",
-                    (cx, cy),
-                    textcoords="offset points",
-                    xytext=(5, 5),
-                    fontsize=7,
-                )
+
+                if self.annotate:
+                    ax.annotate(
+                        f"{gcf:.2f}",
+                        (cx, cy),
+                        textcoords="offset points",
+                        xytext=(5, 5),
+                        fontsize=max(4, 7 - n_tips * 0.01),
+                    )
 
                 if (entry["fdr_p"] is not None and entry["fdr_p"] < 0.05
                         and entry["favored_alt"] is not None):
                     ax.scatter(cx, cy, s=100, c="red", marker="*", zorder=5)
 
-            # Colorbar
-            sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
-            sm.set_array([])
-            cbar = fig.colorbar(sm, ax=ax, pad=0.15)
-            cbar.set_label("Asymmetry ratio")
+            # Colorbar (hide if legend-position is none)
+            legend_loc = config.legend_position or "upper right"
+            if legend_loc != "none":
+                sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+                sm.set_array([])
+                cbar = fig.colorbar(sm, ax=ax, pad=0.15)
+                cbar_fontsize = config.axis_fontsize if config.axis_fontsize else 10
+                cbar.set_label("Asymmetry ratio", fontsize=cbar_fontsize)
 
             if config.show_title:
                 ax.set_title(config.title or "Discordance Asymmetry", fontsize=config.title_fontsize)
@@ -409,16 +418,18 @@ class DiscordanceAsymmetry(Tree):
                 x = node_x.get(id(clade), 0)
                 y = node_y.get(id(clade), 0)
 
-                # Show gCF value
+                # Show gCF value (only if --annotate)
                 total = entry["n_concordant"] + entry["n_alt1"] + entry["n_alt2"]
                 gcf = entry["n_concordant"] / total if total > 0 else 1.0
-                ax.annotate(
-                    f"gCF={gcf:.2f}",
-                    (x, y),
-                    textcoords="offset points",
-                    xytext=(5, 5),
-                    fontsize=7,
-                )
+
+                if self.annotate:
+                    ax.annotate(
+                        f"{gcf:.2f}",
+                        (x, y),
+                        textcoords="offset points",
+                        xytext=(5, 5),
+                        fontsize=max(4, 7 - n_tips * 0.01),
+                    )
 
                 # Mark significant branches (FDR < 0.05)
                 if (entry["fdr_p"] is not None and entry["fdr_p"] < 0.05
@@ -426,13 +437,15 @@ class DiscordanceAsymmetry(Tree):
                     ax.scatter(x, y, s=100, c="red", marker="*", zorder=5)
 
             # Tip labels
-            max_x = max(node_x.values()) if node_x else 0
-            offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                max_x = max(node_x.values()) if node_x else 0
+                offset = max_x * 0.02
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -450,11 +463,14 @@ class DiscordanceAsymmetry(Tree):
                 if color_legend:
                     ax.legend(handles=color_legend, loc="upper right", fontsize=8, frameon=True)
 
-            # Colorbar
-            sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
-            sm.set_array([])
-            cbar = fig.colorbar(sm, ax=ax, pad=0.15)
-            cbar.set_label("Asymmetry ratio")
+            # Colorbar (hide if legend-position is none)
+            legend_loc = config.legend_position or "upper right"
+            if legend_loc != "none":
+                sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+                sm.set_array([])
+                cbar = fig.colorbar(sm, ax=ax, pad=0.15)
+                cbar_fontsize = config.axis_fontsize if config.axis_fontsize else 10
+                cbar.set_label("Asymmetry ratio", fontsize=cbar_fontsize)
 
             ax.set_xlabel("Branch length (subs/site)")
             ax.set_yticks([])

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/phenogram.py

@@ -487,12 +487,14 @@ class Phenogram(Tree):
         # Label tips with taxon names (offset to the right)
         max_x = max(node_x.values()) if node_x else 0
         offset = max_x * 0.02
-        for tip in tips:
-            if id(tip) in node_x and tip.name in trait_values:
-                ax.text(
-                    node_x[id(tip)] + offset, trait_values[tip.name],
-                    tip.name, va="center", fontsize=9,
-                )
+        label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+        if label_fontsize > 0:
+            for tip in tips:
+                if id(tip) in node_x and tip.name in trait_values:
+                    ax.text(
+                        node_x[id(tip)] + offset, trait_values[tip.name],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
         ax.set_xlabel("Distance from root")
         ax.set_ylabel("Trait value")

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/rate_heterogeneity.py

@@ -759,7 +759,9 @@ class RateHeterogeneity(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.02)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.02)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -825,11 +827,13 @@ class RateHeterogeneity(Tree):
 
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/stochastic_character_map.py

@@ -600,7 +600,9 @@ class StochasticCharacterMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -677,11 +679,13 @@ class StochasticCharacterMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.74}/phykit/services/tree/trait_rate_map.py

@@ -544,9 +544,11 @@ class TraitRateMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(
-                ax, tree, coords, fontsize=9, offset=max_x * 0.03
-            )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(
+                    ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03
+                )
 
             # Color annotations
             if self.plot_config.color_file:
@@ -611,11 +613,13 @@ class TraitRateMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Color annotations
             if self.plot_config.color_file:

phykit-2.1.74/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.74"

{phykit-2.1.73 → phykit-2.1.74}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.73
+Version: 2.1.74
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

phykit-2.1.73/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.73"