tSNE script for VSD as input to visualize clusters in sequencing data

tsne.py

import sys
import numpy as np
from sklearn.manifold import TSNE


my_data = np.genfromtxt(str(sys.argv[1]), delimiter=',')

model = TSNE(n_components=2, random_state=0,perplexity=int(sys.argv[2]))
tsne = model.fit_transform(np.transpose(my_data))
np.savetxt(str(sys.argv[3]), tsne, delimiter=",")