Merge pull request #46 from loucerac/ass_crossplot

Ass crossplot

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [year] [fullname]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

drexml/cli/cli.py

@@ -18,7 +18,7 @@
 import click
 import joblib
 
-from drexml.plotting import plot_stability
+from drexml.plotting import plot_metrics
 from drexml.utils import (
     get_data,
     get_number_cuda_devices,
@@ -271,7 +271,7 @@ def run(ctx, **kwargs):
 def plot(ctx, stab_path):
     """Plot the stability results"""
 
-    plot_stability(stab_path)
+    plot_metrics(stab_path)
 
 
 @main.command()

drexml/plotting.py

@@ -128,6 +128,7 @@ def plot_r2_ax(ax_right, data):
 
 def plot_stability(input_path, output_path=None):
     """Plot the stability results."""
+
     print(input_path)
     print(output_path)
     input_path = pathlib.Path(input_path)
@@ -172,3 +173,63 @@ def plot_stability(input_path, output_path=None):
         output_path.joinpath(f"{input_path.stem}.png"), dpi=300, bbox_inches="tight"
     )
     plt.savefig(output_path.joinpath(f"{input_path.stem}.pdf"), bbox_inches="tight")
+
+
+def plot_metrics(input_path, output_folder=None, width=2.735):
+    """Plot stability versus R^2 with 95% CI"""
+
+    input_path = pathlib.Path(input_path).absolute()
+    if output_folder is None:
+        output_folder = input_path.parent
+    else:
+        output_folder = pathlib.Path(output_folder)
+
+    results_df = pd.read_csv(input_path, sep="\t").fillna(0)
+    results_df["r2_error"] = 1.96 * results_df.r2_std / 2
+    results_df = results_df.sort_values(by="stability", ascending=True).reset_index()
+
+    custom_params = {
+        "axes.spines.right": False,
+        "axes.spines.top": False,
+        "axes.spines.left": False,
+        "axes.spines.bottom": False,
+    }
+    sns.set_theme(
+        style="whitegrid", palette="colorblind", context="paper", rc=custom_params
+    )
+
+    fig, ax = plt.subplots(1, 1)
+
+    plt.scatter(results_df.stability, results_df.r2_mean, s=1)
+    plt.errorbar(
+        results_df.stability,
+        results_df.r2_mean,
+        yerr=results_df.r2_error,
+        linestyle="None",
+        linewidth=1,
+        label=r"$R^2$ mean 95% CI",
+    )
+    plt.errorbar(
+        results_df.stability,
+        results_df.r2_mean,
+        xerr=results_df.stability - results_df.stability_lower_95ci,
+        linestyle="None",
+        linewidth=1,
+        label="Stability 95% CI",
+    )
+
+    ax.axvspan(0, 0.4, color="red", alpha=0.1)
+    ax.axvspan(0.4, 0.75, color="y", alpha=0.1)
+    ax.axvspan(0.75, 1.0, color="g", alpha=0.1)
+    ax.set_xticks([0, 0.4, 0.75, 1])
+
+    plt.xlabel("Stability")
+    plt.ylabel(r"$R^2$ score")
+    plt.legend()
+
+    fig.tight_layout()
+    fig.set_size_inches(width, (width * 3) / 4)
+
+    fname = "stability_results_symbol"
+    plt.savefig(output_folder.joinpath(f"{fname}.png"), dpi=300, bbox_inches="tight")
+    plt.savefig(output_folder.joinpath(f"{fname}.pdf"), bbox_inches="tight")

makefile

@@ -8,7 +8,8 @@ all: install format test
 
 install:
 ifeq ($(use_gpu),1)
-	conda create -y -p ./.venv --override-channels -c "nvidia/label/cuda-11.8.0" -c conda-forge cuda cuda-nvcc cuda-toolkit gxx=11.2 python=3.10
+	conda create -y -p ./.venv --override-channels -c "nvidia/label/cuda-11.8.0" \
+	-c conda-forge cuda cuda-nvcc cuda-toolkit gxx=11.2 python=3.10
 else
 	conda create -y -p ./.venv --override-channels -c conda-forge python=3.10
 endif

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "drexml"
-version = "0.9.6"
+version = "0.9.7"
 description = "(DRExM³L) Drug REpurposing using and eXplainable Machine Learning and Mechanistic Models of signal transduction\""
 authors = [
     "Carlos Loucera <[email protected]>",

tests/test_datasets.py

@@ -15,6 +15,7 @@
 from drexml.datasets import get_disease_data, load_df
 from drexml.utils import check_gputree_availability
 
+PLOTTING_EXTENSIONS = ["pdf", "png"]
 N_GPU_LST = [-1, 0] if check_gputree_availability() else [0]
 
 DATA_NAMES = [
@@ -126,6 +127,7 @@ def test_cli_run(n_gpus):
 
     plot_files = [
         ml_folder_expected.joinpath(f"{x.stem}_symbol.png")
+        for ext in PLOTTING_EXTENSIONS
         for x in exist_files
         if "stability" in x.stem
     ]