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@monogenea

monogenea/3-umap.py

Last active Oct 11, 2020
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# Remove expression features with > 50% zero-valued expression levels
is_expressed = np.apply_along_axis(lambda x: np.mean(x == 0) < .5, arr=matrix, axis=0)
matrix = matrix[:,is_expressed.tolist()]
# Log2-transform
matrix = np.log2(matrix.to_numpy() + 1)
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