scRNA-seq_analysis

tools/umap/umap_compute.py

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+import sys
+args = sys.argv
+
+pca_data_fname = args[1]
+umap_coordinates_fname = args[2]
+
+import pandas as pd
+import umap
+    
+print("Loading data ...")
+pca = pd.read_csv(pca_data_fname, sep = ",", index_col = 0).values
+
+print("creating UMAP ... ")
+embedding = umap.UMAP(n_neighbors = 5, min_dist = .3, metric = "correlation", random_state = 17)
+embedding = embedding.fit_transform(pca)
+
+print("saving UMAP coordinates to disk ...")
+df = pd.DataFrame(embedding)
+df.columns = ["UMAPx", "UMAPy"]
+df.to_csv(umap_coordinates_fname)