Updates to Ramachandran plot

bin/sample.py

@@ -11,7 +11,10 @@ from typing import *
 
 import numpy as np
 import pandas as pd
+import mpl_scatter_density
 from matplotlib import pyplot as plt
+from astropy.visualization import LogStretch
+from astropy.visualization.mpl_normalize import ImageNormalize
 
 import torch
 
@@ -93,14 +96,29 @@ def write_preds_pdb_folder(
 
 
 def plot_ramachandran(
-    phi_values, psi_values, fname: str, annot_ss: bool = False, title: str = ""
+    phi_values,
+    psi_values,
+    fname: str,
+    annot_ss: bool = False,
+    title: str = "",
+    plot_type: Literal["kde", "density_heatmap"] = "density_heatmap",
 ):
     """Create Ramachandran plot for phi_psi"""
-    fig = plotting.plot_joint_kde(
-        phi_values,
-        psi_values,
-    )
-    ax = fig.axes[0]
+    if plot_type == "kde":
+        fig = plotting.plot_joint_kde(
+            phi_values,
+            psi_values,
+        )
+        ax = fig.axes[0]
+        ax.set_xlim(-3.67, 3.67)
+        ax.set_ylim(-3.67, 3.67)
+    elif plot_type == "density_heatmap":
+        fig = plt.figure(dpi=800)
+        ax = fig.add_subplot(1, 1, 1, projection="scatter_density")
+        norm = ImageNormalize(vmin=0.0, vmax=650, stretch=LogStretch())
+        ax.scatter_density(phi_values, psi_values, norm=norm, cmap=plt.cm.Blues)
+    else:
+        raise NotImplementedError(f"Cannot plot type: {plot_type}")
     if annot_ss:
         # https://matplotlib.org/stable/tutorials/text/annotations.html
         ram_annot_arrows = dict(
@@ -110,7 +128,7 @@ def plot_ramachandran(
             r"$\alpha$ helix, LH",
             xy=(1.2, 0.5),
             xycoords="data",
-            xytext=(2.0, 1.2),
+            xytext=(1.7, 1.2),
             textcoords="data",
             arrowprops=ram_annot_arrows,
             horizontalalignment="left",
@@ -121,7 +139,7 @@ def plot_ramachandran(
             r"$\alpha$ helix, RH",
             xy=(-1.1, -0.6),
             xycoords="data",
-            xytext=(-1.9, -1.9),
+            xytext=(-1.7, -1.9),
             textcoords="data",
             arrowprops=ram_annot_arrows,
             horizontalalignment="right",
@@ -132,18 +150,15 @@ def plot_ramachandran(
             r"$\beta$ sheet",
             xy=(-1.67, 2.25),
             xycoords="data",
-            xytext=(-0.9, 3.33),
+            xytext=(-0.9, 2.9),
             textcoords="data",
             arrowprops=ram_annot_arrows,
             horizontalalignment="left",
             verticalalignment="center",
             fontsize=14,
         )
-    ax.set_xlabel("$\phi$", fontsize=14)
-    ax.set_ylabel("$\psi$", fontsize=14)
-    ax.set(
-        xlim=(-3.67, 3.67), ylim=(-3.67, 3.67)
-    )
+    ax.set_xlabel("$\phi$ (radians)", fontsize=14)
+    ax.set_ylabel("$\psi$ (radians)", fontsize=14)
     if title:
         ax.set_title(title, fontsize=16)
     fig.savefig(fname, bbox_inches="tight")

bin/sample_plotting_only.py

@@ -31,6 +31,7 @@ from sample import (
 from foldingdiff import custom_metrics as cm
 from foldingdiff.angles_and_coords import get_pdb_length
 
+
 def int_getter(x: str) -> int:
     """Fetches integer value out of a string"""
     matches = re.findall(r"[0-9]+", x)
@@ -54,21 +55,16 @@ def main(dir_name: Path):
     # Filter by test set sequence length
     test_dset_seq_lens = np.array([get_pdb_length(f) for f in test_dset.filenames])
     short_enough_idx = np.where(test_dset_seq_lens <= test_dset.pad)[0]
-    logging.info(f"{len(short_enough_idx)}/{len(test_dset)} test set seqeunces < {test_dset.pad} residues")
+    logging.info(
+        f"{len(short_enough_idx)}/{len(test_dset)} test set seqeunces < {test_dset.pad} residues"
+    )
 
-    # Ramachandran for test set
     select_by_attn = lambda x: x["angles"][x["attn_mask"] != 0]
     test_values = [
         select_by_attn(test_dset.dset.__getitem__(i, ignore_zero_center=True))
         for i in short_enough_idx
     ]
     test_values_stacked = torch.cat(test_values, dim=0).cpu().numpy()
-    plot_ramachandran(
-        test_values_stacked[:, phi_idx],
-        test_values_stacked[:, psi_idx],
-        annot_ss=True,
-        fname=plotdir / "ramachandran_test_annot.pdf",
-    )
 
     # Read in the sampled angles
     sampled_fnames = sorted(
@@ -83,11 +79,23 @@ def main(dir_name: Path):
     logging.info(f"Found {len(sampled_dfs)} sets of generated angles")
 
     sampled_stacked = np.vstack([df.values for df in sampled_dfs])
+    # Ramachandran fro training set
     plot_ramachandran(
         sampled_stacked[:, phi_idx],
         sampled_stacked[:, psi_idx],
         fname=plotdir / "ramachandran_generated.pdf",
     )
+    # Ramachandran for test set, subsampled to be same length
+    rng = np.random.default_rng(seed=6489)
+    ram_idx = rng.choice(
+        len(test_values_stacked), size=len(sampled_stacked), replace=True
+    )
+    plot_ramachandran(
+        test_values_stacked[ram_idx, phi_idx],
+        test_values_stacked[ram_idx, psi_idx],
+        annot_ss=True,
+        fname=plotdir / "ramachandran_test_annot.pdf",
+    )
 
     # Plot distribution overlap
     multi_fig, multi_axes = plt.subplots(dpi=300, nrows=2, ncols=3, figsize=(13, 6.5))