ValueError: setting an array element with a sequence when trying to plot with matplotlib

Question

When I was trying to run the following code:

from matplotlib import pyplot as plt

Xpos = df[df['bound']==1]
Xneg = df[df['bound']==0]
y1, X1 = Xpos['Id'].values, Xpos['seq'].values
y2, X2 = Xneg['Id'].values, Xneg['seq'].values

fig, ax = plt.subplots()
ax.plot(y1, X1 , label='bounded sequences', color='blue')
ax.plot(y2, X2 , label='unbounded sequences', color='red')
plt.show()

I got this error:ValueError: setting an array element with a sequence.
The sample output of df is like the one you find here.
Can anyone help?
Thanks.

Molessia · Accepted Answer · 2020-05-25 13:10:09Z

1

the issue here is that you are trying to plot a list of lists.

For the purpose of explaining you the issue, I created a sample dataset similar to the one you are using (the only difference is that the sequences are shorter). Here is the code that I'm using to create the dataset:

df_dict = {
    "Id": [0, 1, 2, 3, 4],
    "seq": [[0, 0, 1, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 1, 0], [0, 0, 1, 0]],
    "bound": [1, 0, 1, 0, 1]
}
df = pd.DataFrame(df_dict)

If we now execute the first part of your code and print the X1 variable:

Xpos = df[df['bound']==1]
Xneg = df[df['bound']==0]
y1, X1 = Xpos['Id'].values, Xpos['seq'].values
y2, X2 = Xneg['Id'].values, Xneg['seq'].values
print(X1)

The output will be:

[list([0, 0, 1, 0]) list([0, 0, 1, 0]) list([0, 0, 1, 0])]

If what you would like to plot for X1 is the concatenation of each list, e.g. [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0], this might solve your problem:

import pandas as pd
from matplotlib import pyplot as plt

df_dict = {
    "Id": [0, 1, 2, 3, 4],
    "seq": [[0, 0, 1, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 1, 0], [0, 0, 1, 0]],
    "bound": [1, 0, 1, 0, 1]
}
df = pd.DataFrame(df_dict)

Xpos = df[df['bound']==1]
Xneg = df[df['bound']==0]
print(Xpos)
y1, X1 = Xpos['Id'].values, [elem for sub_list in Xpos['seq'].values for elem in sub_list]
y2, X2 = Xneg['Id'].values, [elem for sub_list in Xneg['seq'].values for elem in sub_list]
print(y1)
print(X1)
fig, ax = plt.subplots()
ax.plot(X1, label='bounded sequences', color='blue')
ax.plot(X2, label='unbounded sequences', color='red')
plt.show()

If you want a scatter plot instead of a line plot, you just need to replace the two ax.plot functions with the following:

ax.scatter(range(len(X1)), X1, label='bounded sequences', color='blue')
ax.scatter(range(len(X2)), X2, label='unbounded sequences', color='red')

edited May 25, 2020 at 13:10

answered May 25, 2020 at 9:59

Molessia

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6 Comments

R. Marolahy Over a year ago

Thank you for your reply. What I want to do is to plot X1 and X2 which are equivalent to the bounded sequences (df[df['bound']==1]) and the unbounded sequences ( df[df['bound']==0]) respectively.

Molessia Over a year ago

In this case for example, X1 is [list([0, 0, 1, 0]) list([0, 0, 1, 0]) list([0, 0, 1, 0])] as shown above. Just to clarify, the values that you would like to plot for X1 should be the concatenation of each list, e,g, [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0]?

R. Marolahy Over a year ago

Exactly, and I have already tried that with [int(j) for i in X1 for j in i] but I don't know where the error is?

Molessia Over a year ago

I have edited the answer in order to include a possible solution for this issue, please let me know if this is what you were looking for.

R. Marolahy Over a year ago

works fine, but what I want is a scatter plot of bounded and unbounded sequences instead. Thanks.

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