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Jun 19th, 2019
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  1. ABCA1, ABCA3, TEME
  2.  
  3. df = pd.read_csv('Genes.csv', index_col=0)
  4. X = df.values
  5. means = X.mean(axis=0)
  6. stdevs = X.std(axis=0)
  7. Xcent = X - means
  8. Xnorm = Xcent / stdevs
  9. features = ['ABCA1', 'ABCA3', ..., 'TEME'] #all the genes
  10. df_norm = df.copy()
  11. df_norm[features] = StandardScaler().fit(df_norm[features]).transform(df_norm[features])
  12. X_tsne = TSNE(learning_rate=500, n_components=2).fit_transform(df_norm[features])
  13. figure(figsize=(11, 5))
  14. cmap = plt.get_cmap('nipy_spectral')
  15. scatter(X_tsne[:, 0], X_tsne[:, 1])
  16. title('TSNE')
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