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