Python: 'numpy.ndarray' object has no attribute 'violinplot'

Question

I've been working with matplotlib for the past few weeks, learning how to make different graphs and such. I am currently at a stand still. I am working with gene expression data, so I have a csv file that contains 3 columns of data (mutated, frameshift and nonmutated). However, I am attempting to make a violin plot and I keep getting an error:

Traceback (most recent call last):
  File "/home/fmohamed/Documents/violinplot_script.py", line 39, in <module>
    axes.violinplot(all_data,
AttributeError: 'numpy.ndarray' object has no attribute 'violinplot'

I am not sure what I am doing wrong, but my code is located below:

import matplotlib.pyplot as plt
import numpy as np
import csv

#import data:
with open('/home/fmohamed/Documents/oc_data.csv') as csvfile:
    spamreader = csv.reader(csvfile, delimiter = ' ')
    array = []
    for row in spamreader:
           array.append(row)

# sort out bad data:
splitArray = [row[0].split(',') for row in array]
splitArray = [row for row in splitArray if row[0] != '' and row[1] != '' and 
row[2] != '']
descr = splitArray[0]
splitArray.pop(0) #remove the column descriptions from array
all_data = []
for row in splitArray:
    all_data.append(float(row[0]))
    all_data.append(float(row[1]))
    all_data.append(float(row[2]))

all_data = np.array(all_data)

fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(12, 5))

# plot violin plot
axes.violinplot(all_data,
               showmeans=False,
               showmedians=False)
axes.set_title('violin plot')


# adding horizontal grid lines
axes.yaxis.grid(True)
axes.set_xticks([y+1 for y in range(len(all_data))])
axes.set_xlabel('xlabel')
axes.set_ylabel('ylabel')

# add x-tick labels
plt.setp(axes, xticks=[y+1 for y in range(len(all_data))],
     xticklabels=['mutated', 'frameshift', 'nonmutated'])

plt.show()

Thank you all in advance for any help that you can provide.

As the exception message suggests, axes is a NumPy array of 3 Axes objects. You can do axes[0].violinplot(first_dataset) (so you'd need a loop to plot all three datasets). As @chthonicdaemon suggests, look into Seaborn and its FacetGrid objects if you want a way to make that violin plot for all three datasets in a single command. — Mark Dickinson
– Mark Dickinson, Commented Feb 18, 2016 at 19:05
BTW, your all_data array appears to be a single 1d array. Is that what you intended? If so, what's the purpose of your three separate columns in the subplots call? — Mark Dickinson
– Mark Dickinson, Commented Feb 18, 2016 at 19:07

EijiAdachi · Accepted Answer · 2017-05-02 05:04:55Z

1

Check the version of matplotlib, since violinplots are available only since matplotlib 1.4. To check matplotlib version, just type into your python terminal:

>>> import matplotlib
>>> print matplotlib.__version__

answered May 2, 2017 at 5:04

EijiAdachi

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semi-extrinsic · Accepted Answer · 2021-01-28 15:20:03Z

0

I ran into a very similar issue. The problem is that when you add multiple subplots, the axes object is no longer of Matplotlib axis type, but a Numpy array of several such objects.

The solution is to do the call to violinplot in a loop:

for ax in axes:
    ax.violinplot(all_data,
               showmeans=False,
               showmedians=False)
    ax.set_title('violin plot')

Note that if you have both rows and columns >1, you need to have a nested loop since you have a 2D Numpy array.

Of course this just repeats the same plot many times, so you likely want to put several different examples of your all_data into a Numpy array with the same dimensions as axes

answered Jan 28, 2021 at 15:20

semi-extrinsic

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