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- ABCA1, ABCA3, TEME
- df = pd.read_csv('Genes.csv', index_col=0)
- X = df.values
- means = X.mean(axis=0)
- stdevs = X.std(axis=0)
- Xcent = X - means
- Xnorm = Xcent / stdevs
- features = ['ABCA1', 'ABCA3', ..., 'TEME'] #all the genes
- df_norm = df.copy()
- df_norm[features] = StandardScaler().fit(df_norm[features]).transform(df_norm[features])
- X_tsne = TSNE(learning_rate=500, n_components=2).fit_transform(df_norm[features])
- figure(figsize=(11, 5))
- cmap = plt.get_cmap('nipy_spectral')
- scatter(X_tsne[:, 0], X_tsne[:, 1])
- title('TSNE')
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