bella-companion 0.0.45__py3-none-any.whl → 0.0.46__py3-none-any.whl

bella_companion/cli.py

@@ -2,6 +2,7 @@ import argparse
 import os
 from pathlib import Path
 
+import matplotlib.pyplot as plt
 from dotenv import load_dotenv
 
 from bella_companion.eucovid import run_beast as run_eucovid_beast
@@ -21,12 +22,16 @@ def main():
             os.getenv("JAVA_OPTIONS", ""),
             f"-jar {Path(__file__).parent / 'BELLA.jar'}",
             f"-version_file {Path(__file__).parent / 'version.xml'}",
-            "-seed 42",
             "-overwrite",
             "-statefile /tmp/state",
-            "-DFout /dev/null",
         ]
     )
+    plt.rcParams["pdf.fonttype"] = 42
+    plt.rcParams["xtick.labelsize"] = 14
+    plt.rcParams["ytick.labelsize"] = 14
+    plt.rcParams["font.size"] = 14
+    plt.rcParams["figure.constrained_layout.use"] = True
+    plt.rcParams["lines.linewidth"] = 3
 
     parser = argparse.ArgumentParser(
         prog="bella",

bella_companion/eucovid/run_beast.py

@@ -33,79 +33,86 @@ def run_beast():
         ]
     )
 
-    os.makedirs(output_dir / "Nonparametric", exist_ok=True)
-    submit_job(
-        " ".join(
-            [
-                os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D aligned_fasta={msa_file}",
-                f"-prefix {output_dir / 'Nonparametric'}{os.sep}",
-                str(beast_configs_dir / "Nonparametric.xml"),
-            ]
-        ),
-        base_log_dir / "Nonparametric",
-        cpus=128,
-        mem_per_cpu=12000,
-    )
-
-    os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
-    submit_job(
-        " ".join(
-            [
-                os.environ["BELLA_RUN_BEAST_CMD"],
-                all_predictors_data,
-                f"-prefix {output_dir / 'all-predictors-GLM'}{os.sep}",
-                str(beast_configs_dir / "GLM.xml"),
-            ]
-        ),
-        base_log_dir / "all-predictors-GLM",
-        cpus=128,
-        mem_per_cpu=12000,
-    )
+    for seed in range(1, 3):
+        run_beast_cmd = [os.environ["BELLA_RUN_BEAST_CMD"], f"-seed {42 + seed}"]
 
-    os.makedirs(output_dir / "flights-GLM", exist_ok=True)
-    submit_job(
-        " ".join(
-            [
-                os.environ["BELLA_RUN_BEAST_CMD"],
-                flight_predictor_data,
-                f"-prefix {output_dir / 'flights-GLM'}{os.sep}",
-                str(beast_configs_dir / "GLM.xml"),
-            ]
-        ),
-        base_log_dir / "flights-GLM",
-        cpus=128,
-        mem_per_cpu=12000,
-    )
+        """
+        os.makedirs(output_dir / "Nonparametric", exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *run_beast_cmd,
+                    f"-D aligned_fasta={msa_file}",
+                    f"-prefix {output_dir / 'Nonparametric'}{os.sep}{seed}-",
+                    str(beast_configs_dir / "Nonparametric.xml"),
+                ]
+            ),
+            base_log_dir / "Nonparametric" / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )
+        """
 
-    os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
-    submit_job(
-        " ".join(
-            [
-                os.environ["BELLA_RUN_BEAST_CMD"],
-                f'-D layersRange="0,1,2",nodes="16 8"',
-                all_predictors_data,
-                f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}",
-                str(beast_configs_dir / "MLP.xml"),
-            ]
-        ),
-        base_log_dir / "all-predictors-MLP",
-        cpus=128,
-        mem_per_cpu=12000,
-    )
+        os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *run_beast_cmd,
+                    all_predictors_data,
+                    f"-prefix {output_dir / 'all-predictors-GLM'}{os.sep}{seed}-",
+                    str(beast_configs_dir / "GLM.xml"),
+                ]
+            ),
+            base_log_dir / "Nonparametric" / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )
+        """
+        os.makedirs(output_dir / "flights-GLM", exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *run_beast_cmd,
+                    flight_predictor_data,
+                    f"-prefix {output_dir / 'flights-GLM'}{os.sep}{seed}-",
+                    str(beast_configs_dir / "GLM.xml"),
+                ]
+            ),
+            base_log_dir / "Nonparametric" / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )
+        """
 
-    os.makedirs(output_dir / "flights-MLP", exist_ok=True)
-    submit_job(
-        " ".join(
-            [
-                os.environ["BELLA_RUN_BEAST_CMD"],
-                f'-D layersRange="0,1,2",nodes="16 8"',
-                flight_predictor_data,
-                f"-prefix {output_dir / 'flights-MLP'}{os.sep}",
-                str(beast_configs_dir / "MLP.xml"),
-            ]
-        ),
-        base_log_dir / "flights-MLP",
-        cpus=128,
-        mem_per_cpu=12000,
-    )
+        os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *run_beast_cmd,
+                    '-D layersRange="0,1,2",nodes="16 8"',
+                    all_predictors_data,
+                    f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}{seed}-",
+                    str(beast_configs_dir / "MLP.xml"),
+                ]
+            ),
+            base_log_dir / "Nonparametric" / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )
+        """
+        os.makedirs(output_dir / "flights-MLP", exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *run_beast_cmd,
+                    '-D layersRange="0,1,2",nodes="16 8"',
+                    flight_predictor_data,
+                    f"-prefix {output_dir / 'flights-MLP'}{os.sep}{seed}-",
+                    str(beast_configs_dir / "MLP.xml"),
+                ]
+            ),
+            base_log_dir / "Nonparametric" / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )
+        """

bella_companion/platyrrhine/results.py

@@ -4,13 +4,71 @@ from pathlib import Path
 import matplotlib.pyplot as plt
 import numpy as np
 import polars as pl
+from matplotlib.colors import LinearSegmentedColormap, ListedColormap
 from numpy.typing import NDArray
 from phylogenie import draw_tree, get_node_depths, load_newick, load_nexus
 
+DATA_DIR = Path(__file__).parent / "data"
+CHANGE_TIMES = (
+    pl.read_csv(DATA_DIR / "change_times.csv", has_header=False).to_series().to_list()
+)
+
+
+def _plot_marginal_rates(output_dir: Path, trees_file: str | Path):
+    trees = load_newick(trees_file)
+    all_node_depths = [get_node_depths(tree) for tree in trees]
+    max_time = max(max(node_depths.values()) for node_depths in all_node_depths)
+    time_bins = np.array(list(reversed([0.0, *CHANGE_TIMES, max_time])))
+    for tree in trees:
+        for node in tree:
+            node["diversificationRateSP"] = node["birthRateSP"] - node["deathRateSP"]
+
+    for i, rate in enumerate(["birthRateSP", "deathRateSP", "diversificationRateSP"]):
+        marginal_rates: list[list[float]] = [[] for _ in range(len(CHANGE_TIMES) + 1)]
+        for tree, node_depths in zip(trees, all_node_depths):
+            root_age = tree.height
+            for node in tree:
+                if node.parent is None:
+                    marginal_rates[0].append(node[rate])
+                    continue
+                parent_age = root_age - node_depths[node.parent]  # pyright: ignore
+                node_age = root_age - node_depths[node]
+                t1 = np.where(time_bins >= parent_age)[0][-1]
+                t2 = np.where(time_bins > node_age)[0][-1]
+                for t in range(t1, t2 + 1):
+                    marginal_rates[t].append(node[rate])
+
+        median = [float(np.median(rates)) for rates in marginal_rates]
+        lower = [float(np.percentile(rates, 2.5)) for rates in marginal_rates]
+        upper = [float(np.percentile(rates, 97.5)) for rates in marginal_rates]
+        plt.step(  # pyright: ignore
+            time_bins, [median[0], *median], color=f"C{i}", label=type
+        )
+        plt.fill_between(  # pyright: ignore
+            time_bins,
+            [lower[0], *lower],
+            [upper[0], *upper],
+            color=f"C{i}",
+            alpha=0.2,
+            step="pre",
+        )
+
+        plt.gca().invert_xaxis()
+        plt.xlabel("Time (mya)")  # pyright: ignore
+        plt.ylabel(  # pyright: ignore
+            r"$\lambda$"
+            if rate == "birthRateSP"
+            else r"$\mu$"
+            if rate == "deathRateSP"
+            else r"$d$"
+        )
+        plt.savefig(output_dir / f"marginal-{rate}.svg")  # pyright: ignore
+        plt.close()
+
 
 def _plot_tree(output_dir: Path, tree_file: str | Path):
     sample_trees = load_nexus(tree_file)
-    trees = [sample_trees[f"STATE_{i*100_000}"] for i in range(11, 101)]
+    trees = [sample_trees[f"STATE_{i * 100_000}"] for i in range(11, 101)]
 
     for tree in trees:
         for node in tree:
@@ -21,44 +79,63 @@ def _plot_tree(output_dir: Path, tree_file: str | Path):
     for node in avg_tree:
         node.clear()
     for avg_node, nodes in zip(avg_tree, zip(*trees)):
-        avg_node.set("birthRateSP", np.mean([n["birthRateSP"] for n in nodes]))
-        avg_node.set("deathRateSP", np.mean([n["deathRateSP"] for n in nodes]))
+        avg_node["birthRateSP"] = np.mean([n["birthRateSP"] for n in nodes])
+        avg_node["deathRateSP"] = np.mean([n["deathRateSP"] for n in nodes])
+        avg_node["diversificationRateSP"] = (
+            avg_node["birthRateSP"] - avg_node["deathRateSP"]
+        )
+        avg_node["type"] = int(np.median([int(n["type"]) for n in nodes]))
 
     avg_tree.ladderize()
-    for rate in ["birthRateSP", "deathRateSP"]:
+    cmaps: dict[str, LinearSegmentedColormap] = {
+        "birthRateSP": plt.cm.Blues,  # pyright: ignore
+        "deathRateSP": plt.cm.Oranges,  # pyright: ignore
+        "diversificationRateSP": plt.cm.Greens,  # pyright: ignore
+        "type": plt.cm.Purples,  # pyright: ignore
+    }
+    for color_by, cm in cmaps.items():
         ax = plt.gca()
-        draw_tree(
-            avg_tree,
-            ax,
-            color_by=rate,
-            hist_axes_kwargs={
-                "loc": "upper left",
-                "bbox_to_anchor": (0.06, 0, 1, 1),
-                "bbox_transform": ax.transAxes,
-            },
-        )
+        if color_by == "type":
+            cmap = ListedColormap(cm(np.linspace(0.3, 1, 4)))  # pyright: ignore
+            draw_tree(
+                avg_tree,
+                ax,
+                color_by=color_by,
+                legend_kwargs={"title": "Body mass", "loc": "upper left"},
+                colormap=cmap,
+            )
+        else:
+            cmap = LinearSegmentedColormap.from_list(
+                "cmap",
+                cm(np.linspace(0.2, 1, 256)),  # pyright: ignore
+            )
+            draw_tree(
+                avg_tree,
+                ax,
+                color_by=color_by,
+                hist_axes_kwargs={
+                    "loc": "upper left",
+                    "bbox_to_anchor": (0.06, 0, 1, 1),
+                    "bbox_transform": ax.transAxes,
+                },
+                colormap=cmap,
+            )
         height = avg_tree.height
         ticks = np.arange(height, 0, -10)
         ax.set_xticks(ticks, [str(round(height - t)) for t in ticks])  # pyright: ignore
-        plt.xlabel("Time (mya)")  # pyright: ignore
-        plt.savefig(output_dir / f"{rate}-tree.svg")  # pyright: ignore
+        ax.set_xlabel("Time (mya)")  # pyright: ignore
+        plt.savefig(output_dir / f"{color_by}-tree.svg")  # pyright: ignore
         plt.close()
 
 
 def _plot_predictions(output_dir: Path, log_summary_file: str | Path):
     log_summary = pl.read_csv(log_summary_file)
 
-    data_dir = Path(__file__).parent / "data"
-    change_times = (
-        pl.read_csv(data_dir / "change_times.csv", has_header=False)
-        .to_series()
-        .to_list()
-    )
     max_time = max(
         max(get_node_depths(tree).values())
-        for tree in load_newick(data_dir / "trees.nwk")
+        for tree in load_newick(DATA_DIR / "trees.nwk")
     )
-    time_bins = list(reversed([0.0, *change_times, max_time]))
+    time_bins = list(reversed([0.0, *CHANGE_TIMES, max_time]))
 
     gradient = np.linspace(0.4, 0.9, 4)
     colors: dict[str, NDArray[np.floating]] = {
@@ -73,14 +150,14 @@ def _plot_predictions(output_dir: Path, log_summary_file: str | Path):
                     [
                         pl.col(f"birthRateSPi{i}_{type}_median")
                         - pl.col(f"deathRateSPi{i}_{type}_median")
-                        for i in range(len(change_times) + 1)
+                        for i in range(len(CHANGE_TIMES) + 1)
                     ]
                 ).to_numpy()
             else:
                 estimates = log_summary.select(
                     [
                         pl.col(f"{rate}i{i}_{type}_median")
-                        for i in range(len(change_times) + 1)
+                        for i in range(len(CHANGE_TIMES) + 1)
                     ]
                 ).to_numpy()
             median = np.median(estimates, axis=0)
@@ -95,8 +172,12 @@ def _plot_predictions(output_dir: Path, log_summary_file: str | Path):
         plt.ylabel(  # pyright: ignore
             r"$\lambda$"
             if rate == "birthRateSP"
-            else r"$\mu$" if rate == "deathRateSP" else r"$d$"
+            else r"$\mu$"
+            if rate == "deathRateSP"
+            else r"$d$"
         )
+        if rate in ["birthRateSP", "deathRateSP"]:
+            plt.ylim(0, 0.4)  # pyright: ignore
         plt.savefig(output_dir / f"{rate}-predictions.svg")  # pyright: ignore
         plt.close()
 
@@ -107,3 +188,4 @@ def plot_platyrrhine_results():
     os.makedirs(output_dir, exist_ok=True)
     _plot_predictions(output_dir, summaries_dir / "MLP.csv")
     _plot_tree(output_dir, summaries_dir / "sample-trees.nexus")
+    _plot_marginal_rates(output_dir, summaries_dir / "trees.nwk")

bella_companion/platyrrhine/run_beast.py

@@ -39,22 +39,23 @@ def run_beast():
         command = " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
+                "-seed 42",
                 f'-D types="{",".join(types)}"',
-                f'-D startTypePriorProbs="0.25 0.25 0.25 0.25"',
-                f"-D birthRateUpper=5",
-                f"-D deathRateUpper=5",
-                f'-D samplingChangeTimes="2.58 5.333 23.03"',
-                f"-D samplingRateUpper=5",
-                f'-D samplingRateInit="2.5 2.5 2.5 2.5"',
-                f"-D migrationRateUpper=5",
-                f'-D migrationRateInit="2.5 0 0 2.5 2.5 0 0 2.5 2.5 0 0 2.5"',
-                f'-D nodes="16 8"',
-                f'-D layersRange="0,1,2"',
+                '-D startTypePriorProbs="0.25 0.25 0.25 0.25"',
+                "-D birthRateUpper=5",
+                "-D deathRateUpper=5",
+                '-D samplingChangeTimes="2.58 5.333 23.03"',
+                "-D samplingRateUpper=5",
+                '-D samplingRateInit="2.5 2.5 2.5 2.5"',
+                "-D migrationRateUpper=5",
+                '-D migrationRateInit="2.5 0 0 2.5 2.5 0 0 2.5 2.5 0 0 2.5"',
+                '-D nodes="16 8"',
+                '-D layersRange="0,1,2"',
                 f"-D treeFile={tree_file}",
                 f"-D treeIndex={i}",
                 f"-D changeTimesFile={change_times_file}",
                 f"-D traitsFile={traits_file}",
-                f"-D traitValueCol=3",
+                "-D traitValueCol=3",
                 f"-D processLength={process_length}",
                 f'-D timePredictor="{time_predictor}"',
                 f'-D log10BMPredictor="{log10BM_predictor}"',

bella_companion/simulations/generate_figures.py

@@ -1,5 +1,3 @@
-import matplotlib.pyplot as plt
-
 from bella_companion.simulations.figures import (
     plot_epi_multitype_results,
     plot_epi_skyline_results,
@@ -10,13 +8,6 @@ from bella_companion.simulations.figures import (
 
 
 def generate_figures():
-    plt.rcParams["pdf.fonttype"] = 42
-    plt.rcParams["xtick.labelsize"] = 14
-    plt.rcParams["ytick.labelsize"] = 14
-    plt.rcParams["font.size"] = 14
-    plt.rcParams["figure.constrained_layout.use"] = True
-    plt.rcParams["lines.linewidth"] = 3
-
     plot_scenarios()
     plot_epi_skyline_results()
     plot_epi_multitype_results()

bella_companion/simulations/run_beast.py

@@ -56,7 +56,11 @@ def run_beast():
                         f"-D lastSampleTime={max(get_node_depths(tree).values())}"
                     )
 
-                base_command = [os.environ["BELLA_RUN_BEAST_CMD"], *beast_args]
+                base_command = [
+                    os.environ["BELLA_RUN_BEAST_CMD"],
+                    "-seed 42",
+                    *beast_args,
+                ]
                 if model in ["Nonparametric", "GLM"]:
                     command = " ".join(
                         [*base_command, str(inference_configs_dir / f"{model}.xml")]

{bella_companion-0.0.45.dist-info → bella_companion-0.0.46.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.45
-Summary: Add your description here
+Version: 0.0.46
+Summary: Bayesian Evolutionary Layered Learning Architectures (BELLA) companion
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: arviz>=0.22.0
 Requires-Dist: bella-lumiere>=0.0.14
 Requires-Dist: dotenv>=0.9.9
-Requires-Dist: phylogenie>=3.1.3
+Requires-Dist: phylogenie>=3.1.4
 Requires-Dist: poetry>=2.2.1
 Requires-Dist: seaborn>=0.13.2

{bella_companion-0.0.45.dist-info → bella_companion-0.0.46.dist-info}/RECORD

@@ -1,11 +1,11 @@
 bella_companion/BELLA.jar,sha256=4mKDzPfz263rTqA9KS2f4Mc-UWGMuj8G48ZDonKSqVw,67408597
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=v2kGrcZ9g448W4Bj-4AU5hwQGmpTRBIbgxhMT8li30s,2786
+bella_companion/cli.py,sha256=CrtV2CG6G1nKCCVu02gtNlpHNJHLnFtSaru-LFiHKKc,3014
 bella_companion/version.xml,sha256=Gr3nsYqFhVNP0Mszl_IfilxefsPN8ZpQlGlB8OJSwnE,522
 bella_companion/__pycache__/__init__.cpython-310.pyc,sha256=OWbv3-oQ0uVrCKYMlnplMpvDhv5Ytf3aYb7Eu_UONkU,151
-bella_companion/__pycache__/cli.cpython-310.pyc,sha256=KbutcYiFHY833JXUWR_zA5md-_XQK58BUPpsfpjTYB4,2425
+bella_companion/__pycache__/cli.cpython-310.pyc,sha256=-k34T2uplWxW_fUrSVadFAYEDos-bvonW2RDeyHuj0A,2680
 bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
-bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
+bella_companion/eucovid/run_beast.py,sha256=vIS0MiRAGYkQyr2qXeOCtNyaN4tkyRrxumCv_WC8vrc,3905
 bella_companion/eucovid/__pycache__/__init__.cpython-310.pyc,sha256=cwLb8j-Jrl5beRcoZEtbpvQlG9KENPuB2F4fa1RBYIQ,248
 bella_companion/eucovid/__pycache__/run_beast.cpython-310.pyc,sha256=jEqqaPBugV7B8YZQjNIgYnhpCwDOV21xyG1N_IbRdJo,1922
 bella_companion/eucovid/beast_configs/GLM.xml,sha256=b5rAeKVEam3u2AGSJsm7EHB6LcC0l9bp1SyZT2QyjpI,10892
@@ -29,13 +29,13 @@ bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv,sha256=Ku39Ts0HW9r5l
 bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5DIaZuc3B0mSs-B3kw3G2zja1LfmL_xLwlNtLDo,280
 bella_companion/platyrrhine/__init__.py,sha256=gySgNPoKaEdhcZppKMsCmS-aAcYw_rDEw0viz72Udaw,259
 bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
-bella_companion/platyrrhine/results.py,sha256=x5NluhwATa136Gb1lEC_tfl7zhFzFaQnOp9ZRO11zhM,3991
-bella_companion/platyrrhine/run_beast.py,sha256=_9Ex2B65zu6I68uY6s3_dohPYPaFP3E7u-uyWuDLAJc,2477
+bella_companion/platyrrhine/results.py,sha256=aRx9MkI43f5bhr-16UkShDH-_oMNFzhHxfU2WK1L3BY,7468
+bella_companion/platyrrhine/run_beast.py,sha256=t1gUmn_HEXKqxgGXYCdohGDWeL-QEpW7r3bKXlRfdog,2494
 bella_companion/platyrrhine/summarize.py,sha256=Qc3GE2vUspTqU_QjLdULvK0r7AZ3JTdqsBmd71izt7M,1356
 bella_companion/platyrrhine/__pycache__/__init__.cpython-310.pyc,sha256=_7OOgWWr8apuTVm7TLhvmP41QHTDFlDNjTtJ9J3vpZc,425
-bella_companion/platyrrhine/__pycache__/results.cpython-310.pyc,sha256=q-9Hd0jDV6WSMI3lL-wiASAxVttekmmJ_FHSOGqaj9c,4028
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@@ -106,11 +106,11 @@ bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENH
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