AttributeError: 'numpy.ndarray' object has no attribute 'get_matrix'

Question

I am trying to plot a wonderful PCA using mlpy, and the c argument to plt.scatter is causing an exception.

dataset: http://mlpy.sourceforge.net/docs/3.5/_downloads/iris.csv

import mlpy
from matplotlib.mlab import PCA
import matplotlib.pyplot as plt
def classification():
 # x: (observations x attributes) matrix
 x = np.array(iris)[:, :4]
 # y: classes (1: setosa, 2: versicolor, 3: virginica)
 outputs_file="/Users/vasques/Desktop/classification.csv"
 y = np.loadtxt(outputs_file, delimiter=',')[:, 4].astype(np.int)
 pca = mlpy.PCA() # new PCA instance
 pca.learn(x) # learn from data
 z = pca.transform(x, k=2) # embed x into the k=2 dimensional subspace
 plt.set_cmap(plt.cm.Paired)
 fig1 = plt.figure(1)
 title = plt.title("PCA")
 plot = plt.scatter(z[:, 0], z[:, 1], c=y)
 labx = plt.xlabel("First component")
 laby = plt.ylabel("Second component")
 plt.show()

and I have the following error:

Traceback (most recent call last):
 File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 59, in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
 File "/Library/Python/2.7/site-packages/matplotlib/figure.py", line 1050, in draw
 func(*args)
 File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 59, in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
 File "/Library/Python/2.7/site-packages/matplotlib/axes/_base.py", line 2075, in draw
 a.draw(renderer)
 File "/Library/Python/2.7/site-packages/matplotlib/collections.py", line 729, in draw
 Collection.draw(self, renderer)
 File "/Library/Python/2.7/site-packages/matplotlib/artist.py", line 59, in draw_wrapper
 draw(artist, renderer, *args, **kwargs)
 File "/Library/Python/2.7/site-packages/matplotlib/collections.py", line 301, in draw
 self._offset_position)
 File "/Library/Python/2.7/site-packages/matplotlib/backends/backend_macosx.py", line 79, in draw_path_collection
 all_transforms = [t.get_matrix() for t in all_transforms]
AttributeError: 'numpy.ndarray' object has no attribute 'get_matrix'

When I delete c=y in plt.scatter it runs but I have a single color that does not allow me to recognize the groups.

• user3091978: and this is exactly the same code as here: mlpy.sourceforge.net/docs/3.5/…
• Iguananaut: Might want to clean up the source code a bit first. For example you define data=np.zeros(shape=(4,4)) and then immediately redefine it to data=np.array(iris); makes it hard to determine what the intent is.
• tacaswell: @user3091978 Can you make a simpler example that is copy-pastable?