I am attempting to generate a scatter plot to show data before and after the PCA transform, similar to this tutorial.
To do this, I am running the following code:
fig, axes = plt.subplots(1,2)
axes[0].scatter(X.iloc[:,0], X.iloc[:,1], c=y)
axes[0].set_xlabel('x1')
axes[0].set_ylabel('x2')
axes[0].set_title('Before PCA')
axes[1].scatter(X_new[:,0], X_new[:,1], c=y)
axes[1].set_xlabel('PC1')
axes[1].set_ylabel('PC2')
axes[1].set_title('After PCA')
plt.show()
Which is causing this error to appear:
ValueError: RGBA values should be within 0-1 range
X is the preprocessed matrix of features, which contains 196 samples and 59 features. Whereas y is the dependent variable and contains two classes [0, 1].
Here is the full error message:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-109-2c4f74ddce3f> in <module>
1 fig, axes = plt.subplots(1,2)
----> 2 axes[0].scatter(X.iloc[:,0], X.iloc[:,1], c=y)
3 axes[0].set_xlabel('x1')
4 axes[0].set_ylabel('x2')
5 axes[0].set_title('Before PCA')
~/anaconda3/lib/python3.7/site-packages/matplotlib/__init__.py in inner(ax, data, *args, **kwargs)
1597 def inner(ax, *args, data=None, **kwargs):
1598 if data is None:
-> 1599 return func(ax, *map(sanitize_sequence, args), **kwargs)
1600
1601 bound = new_sig.bind(ax, *args, **kwargs)
~/anaconda3/lib/python3.7/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, plotnonfinite, **kwargs)
4495 offsets=offsets,
4496 transOffset=kwargs.pop('transform', self.transData),
-> 4497 alpha=alpha
4498 )
4499 collection.set_transform(mtransforms.IdentityTransform())
~/anaconda3/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, paths, sizes, **kwargs)
881 """
882
--> 883 Collection.__init__(self, **kwargs)
884 self.set_paths(paths)
885 self.set_sizes(sizes)
~/anaconda3/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, edgecolors, facecolors, linewidths, linestyles, capstyle, joinstyle, antialiaseds, offsets, transOffset, norm, cmap, pickradius, hatch, urls, offset_position, zorder, **kwargs)
125
126 self._hatch_color = mcolors.to_rgba(mpl.rcParams['hatch.color'])
--> 127 self.set_facecolor(facecolors)
128 self.set_edgecolor(edgecolors)
129 self.set_linewidth(linewidths)
~/anaconda3/lib/python3.7/site-packages/matplotlib/collections.py in set_facecolor(self, c)
676 """
677 self._original_facecolor = c
--> 678 self._set_facecolor(c)
679
680 def get_facecolor(self):
~/anaconda3/lib/python3.7/site-packages/matplotlib/collections.py in _set_facecolor(self, c)
659 except AttributeError:
660 pass
--> 661 self._facecolors = mcolors.to_rgba_array(c, self._alpha)
662 self.stale = True
663
~/anaconda3/lib/python3.7/site-packages/matplotlib/colors.py in to_rgba_array(c, alpha)
277 result[mask] = 0
278 if np.any((result < 0) | (result > 1)):
--> 279 raise ValueError("RGBA values should be within 0-1 range")
280 return result
281 # Handle single values.
ValueError: RGBA values should be within 0-1 range
I am unsure what is causing this error and would appreciate help in figuring this out. Thanks!
The c=
parameter of ax.scatter
can be given in several ways:
[[1,0,0], [0,0,1]]
. All these values need to be between 0 and 1. Moreover, there should be either 3 (for RGB) or 4 (for RGBA) values per entry.["red", "#B789C0", "turquoise"]
"cornflowerblue"
.Now, when an array of numbers is given, to be able to distinguish between the first and the second case, matplotlib just looks at the array dimension. If it is 1D, matplotlib assumes the first case. For 2D, it assumes the second case. Note that also an Nx1
or an 1xN
array is considered 2D. You can use np.squeeze()
to "squeeze out" the dummy second dimension.