add umap script

Author: quentinblampey

.gitignore

@@ -1,3 +1,6 @@
+figures
+explore
+
 # OS related
 .DS_Store
 

novae_benchmark/pan_tissue_umap.py

@@ -0,0 +1,67 @@
+import time
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import scanpy as sc
+import seaborn as sns
+from anndata import AnnData
+
+
+def timing(func):
+    def wrapper(*args, **kwargs):
+        start_time = time.time()
+        func(*args, **kwargs)
+        end_time = time.time()
+        execution_time = end_time - start_time
+        print(f"Execution time: {execution_time} seconds")
+        return execution_time
+
+    return wrapper
+
+
+title_dict = {
+    "tissue": "Tissue",
+    "technology": "Technology",
+    "domain": "Domain",
+}
+
+
+@timing
+def compute_and_save_umap(adata: AnnData, res_path: Path):
+    print(f"{adata.n_obs=}")
+
+    sc.pp.neighbors(adata, use_rep="novae_latent_corrected")
+    sc.tl.umap(adata)
+
+    colors = []
+    for key in ["domain", "tissue", "technology", "novae_domains_15", "novae_domains_20", "novae_domains_25"]:
+        if key in adata.obs:
+            colors.append(key)
+
+    for color in colors:
+        sc.pl.umap(adata, color=color, show=False, title=title_dict.get(color, color))
+        sns.despine(offset=10, trim=True)
+        plt.savefig(res_path / f"umap_{adata.n_obs}_{color}.png", bbox_inches="tight", dpi=300)
+
+
+def main():
+    # data_path = Path("/Users/quentinblampey/dev/novae/data/results/dry-wood-40")
+    # res_path = Path("/Users/quentinblampey/dev/novae_benchmark/figures")
+    data_path = Path("/gpfs/workdir/blampeyq/novae/data/results/zany-night-17")
+    res_path = Path("/gpfs/workdir/blampeyq/novae_benchmark/figures")
+
+    adata_full = sc.read_h5ad(data_path / "adata_conc.h5ad")
+
+    print("adata:", adata_full)
+
+    for n_obs in [1_000, 1_000_000, 10_000_000, None]:
+        if n_obs is not None and n_obs < adata_full.n_obs:
+            adata = sc.pp.subsample(adata_full, n_obs=n_obs, copy=True)
+        else:
+            adata = adata_full
+
+        compute_and_save_umap(adata, res_path)
+
+
+if __name__ == "__main__":
+    main()

remote/umaps.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+#SBATCH --job-name=novae
+#SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
+#SBATCH --mem=128G
+#SBATCH --time=24:00:00
+#SBATCH --cpus-per-task=2
+#SBATCH --partition=cpu_long
+
+module purge
+module load anaconda3/2022.10/gcc-11.2.0
+source activate novae
+
+cd /gpfs/workdir/blampeyq/novae_benchmark
+
+python -u novae_benchmark/pan_tissue_umap.py