CH01_SEC05_2_OvarianCancer.ipynb

Kernel: Python 3

import matplotlib.pyplot as plt
import numpy as np
import os
from mpl_toolkits.mplot3d import Axes3D
plt.rcParams['figure.figsize'] = [16, 8]
plt.rcParams.update({'font.size': 18})


obs = np.loadtxt(os.path.join('..','DATA','ovariancancer_obs.csv'),delimiter=',')

f = open(os.path.join('..','DATA','ovariancancer_grp.csv'), "r")
grp = f.read().split("\n")

U, S, VT = np.linalg.svd(obs,full_matrices=0)

fig1 = plt.figure()
ax1 = fig1.add_subplot(121)
ax1.semilogy(S,'-o',color='k')
ax2 = fig1.add_subplot(122)
ax2.plot(np.cumsum(S)/np.sum(S),'-o',color='k')

plt.show()

fig2 = plt.figure()
ax = fig2.add_subplot(111, projection='3d')

for j in range(obs.shape[0]):
    x = VT[0,:] @ obs[j,:].T
    y = VT[1,:] @ obs[j,:].T
    z = VT[2,:] @ obs[j,:].T
    
    if grp[j] == 'Cancer':
        ax.scatter(x,y,z,marker='x',color='r',s=50)
    else:
        ax.scatter(x,y,z,marker='o',color='b',s=50)

ax.view_init(25,20)
plt.show()