Hi,
Im trying to plot a PCA chart using biopython.
I’m new to biopython and python in general so excuse me if my code doesnt look good.
I tried to do something like that:
from Bio.Cluster import pca
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
#PCA chart
with open('heat2forpca.csv', 'r', encoding='mac_roman', newline="") as csvfile2:
df2 = pd.read_csv(csvfile2, sep=',').fillna(0)
columnmean, coordinates, components, eigenvalues = pca(df2)
plt.plot(pca(df2))
plt.show()
but I get this error:
Traceback (most recent call last):
File "C:UsersLenovoDesktopthird yearflowerprojectuntitled0.py", line 72, in <module>
columnmean, coordinates, components, eigenvalues = pca(df2)
File "C:UsersLenovoanaconda3libsite-packagesBioCluster__init__.py", line 621, in pca
_cluster.pca(data, columnmean, coordinates, pc, eigenvalues)
RuntimeError: data is not contiguous
my dataframe looks like this:
print(df2)
Unknown ... Triacontanoic acid methyl ester
0 1082585 ... 143327
1 958408 ... 111371
2 1067961 ... 97396
3 1072394 ... 111287
4 917288 ... 79464
.. ... ... ...
100 619474 ... 99796
101 339709 ... 88881
102 331859 ... 74320
103 543078 ... 67988
104 378728 ... 57975
[105 rows x 140 columns]
any kind of help will be appreciated!