scatter color vs c

[smartinsightsfromdata]

The following code gives error, but works replacing color= withc=
I suspect is either a bug, or some piece of documentation missing?

I'm using:
matplotlib 1.5.3
pandas 0.19.1
python 3.5

import pandas as pd
import numpy as np
from sklearn.datasets import load_iris
%matplotlib inline

iris = load_iris()
colors = list()
palette = {0: "red", 1: "green", 2: "blue"}

for c in np.nditer(iris.target): colors.append(palette[int(c)])
    # using the palette dictionary, we convert
    # each numeric class into a color string
dataframe = pd.DataFrame(iris.data,
columns=iris.feature_names)
scatterplot = pd.scatter_matrix(dataframe, alpha=0.3,
figsize=(10, 10), diagonal='hist', color=colors, marker='o', grid=True)

[tacaswell]

Can you reproduce this with out using pandas? Otherwise this probably should be reported against pandas.

[tacaswell]

Can you also include the full traceback?

[smartinsightsfromdata]

This is the full trace:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-4-f3d30057e124> in <module>()
     14 columns=iris.feature_names)
     15 scatterplot = pd.scatter_matrix(dataframe, alpha=0.3,
---> 16 figsize=(10, 10), diagonal='hist', color=colors, marker='o', grid=True)

/Users/e/anaconda/lib/python3.5/site-packages/pandas/tools/plotting.py in scatter_matrix(frame, alpha, figsize, ax, grid, diagonal, marker, density_kwds, hist_kwds, range_padding, **kwds)
    393 
    394                 ax.scatter(df[b][common], df[a][common],
--> 395                            marker=marker, alpha=alpha, **kwds)
    396 
    397                 ax.set_xlim(boundaries_list[j])

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in inner(ax, *args, **kwargs)
   1817                     warnings.warn(msg % (label_namer, func.__name__),
   1818                                   RuntimeWarning, stacklevel=2)
-> 1819             return func(ax, *args, **kwargs)
   1820         pre_doc = inner.__doc__
   1821         if pre_doc is None:

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, **kwargs)
   3787                 facecolors = co
   3788             if c is not None:
-> 3789                 raise ValueError("Supply a 'c' kwarg or a 'color' kwarg"
   3790                                  " but not both; they differ but"
   3791                                  " their functionalities overlap.")

ValueError: Supply a 'c' kwarg or a 'color' kwarg but not both; they differ but their functionalities overlap.

[smartinsightsfromdata]

I tried with just matpltlib. As before c works and color doesn't, but I get a different error.

Incidentally, I couldn't find anywhere the reference on the difference between color kwargs and c kwargs mentioned in the trace.

import numpy as np
import matplotlib.pyplot as plt
N = 50
x = np.random.rand(N)
y = np.random.rand(N)
colors = np.random.rand(N)
area = np.pi * (15 * np.random.rand(N))**2  # 0 to 15 point radiuses
plt.scatter(x, y, s=area, color=colors, alpha=0.5)

This is the trace:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/colors.py in to_rgba(self, arg, alpha)
    367                     raise ValueError(
--> 368                             'length of rgba sequence should be either 3 or 4')
    369             else:

ValueError: length of rgba sequence should be either 3 or 4

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/colors.py in to_rgba_array(self, c, alpha)
    398             # Single value? Put it in an array with a single row.
--> 399             return np.array([self.to_rgba(c, alpha)], dtype=np.float)
    400         except ValueError:

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/colors.py in to_rgba(self, arg, alpha)
    375             raise ValueError(
--> 376                 'to_rgba: Invalid rgba arg "%s"\n%s' % (str(arg), exc))
    377 

ValueError: to_rgba: Invalid rgba arg "[ 0.51212644  0.22378055  0.06807402  0.43638562  0.68215248  0.1378158
  0.15249078  0.55415346  0.47947919  0.12748865  0.72954419  0.37898197
  0.42483739  0.1797149   0.59384571  0.54982906  0.05255149  0.4734899
  0.90948923  0.08066408  0.22102738  0.77243848  0.05687152  0.38126391
  0.05717766  0.3300619   0.81012634  0.60052149  0.46439006  0.86098937
  0.93625576  0.16322075  0.14090725  0.88908521  0.32210086  0.55698194
  0.18936879  0.7390388   0.03459946  0.85838907  0.22985901  0.15620236
  0.58757227  0.96806694  0.58318205  0.00226799  0.00164644  0.2462151
  0.9577508   0.57849709]"
length of rgba sequence should be either 3 or 4

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, **kwargs)
   3777             try:
-> 3778                 mcolors.colorConverter.to_rgba_array(co)
   3779             except ValueError:

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/colors.py in to_rgba_array(self, c, alpha)
    402                 if c.ndim != 2 and c.dtype.kind not in 'SU':
--> 403                     raise ValueError("Color array must be two-dimensional")
    404                 if (c.ndim == 2 and c.shape[1] == 4 and c.dtype.kind == 'f'):

ValueError: Color array must be two-dimensional

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-9-68c680282e55> in <module>()
      9 area = np.pi * (15 * np.random.rand(N))**2  # 0 to 15 point radiuses
     10 
---> 11 plt.scatter(x, y, s=area, color=colors, alpha=0.5)

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/pyplot.py in scatter(x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, hold, data, **kwargs)
   3256                          vmin=vmin, vmax=vmax, alpha=alpha,
   3257                          linewidths=linewidths, verts=verts,
-> 3258                          edgecolors=edgecolors, data=data, **kwargs)
   3259     finally:
   3260         ax.hold(washold)

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/__init__.py in inner(ax, *args, **kwargs)
   1817                     warnings.warn(msg % (label_namer, func.__name__),
   1818                                   RuntimeWarning, stacklevel=2)
-> 1819             return func(ax, *args, **kwargs)
   1820         pre_doc = inner.__doc__
   1821         if pre_doc is None:

/Users/e/anaconda/lib/python3.5/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, **kwargs)
   3778                 mcolors.colorConverter.to_rgba_array(co)
   3779             except ValueError:
-> 3780                 raise ValueError("'color' kwarg must be an mpl color"
   3781                                  " spec or sequence of color specs.\n"
   3782                                  "For a sequence of values to be"

ValueError: 'color' kwarg must be an mpl color spec or sequence of color specs.
For a sequence of values to be color-mapped, use the 'c' kwarg instead.

[efiring]

ValueError: 'color' kwarg must be an mpl color spec or sequence of color specs.
For a sequence of values to be color-mapped, use the 'c' kwarg instead.

That last exception message is telling you what the problem is, and how to fix it, so matplotlib is behaving as intended. I don't know what the problem is on the pandas side.

[goyodiaz]

It looks like a pandas issue. pandas.scatter_matrix always pass c to scatter but the caller can optionally pass more keywords arguments, including color. If the caller pass only color then scatter_matrix will pass both c and color and matplotlib will raise with a message that is confusing to the user because they did not pass c. Probably scatter_matrix should either raise with a clearer message or drop the c keyword argument when the user pass color.

There is still a potential source of confusion in the matplotlib side. I guess many users will use color instead of c because in other functions like plot they are equivalent. Maybe a comment should be added to the scatter docstring stating that c and color are actually different and incompatible.

[smartinsightsfromdata]

@goyodiaz Thanks of the comment.
Before this error I didn't have it clear that c and color where different and some clarification in the docs would help.

I will also raise this error on pandas.

[Kojoley]

Closed as not a matplotlib issue.

[corner100]

This is working:

x = rng.randn(12)
y = rng.randn(12)
colors = rng.rand(12)
sizes = 1000 * rng.rand(12)

plt.scatter(x, y, c=colors, s=sizes, alpha=0.3,
            cmap='viridis')
plt.colorbar();  # show color scale
plt.show()

This is not working:

x = rng.randn(12)
y = rng.randn(12)
colors = rng.rand(12)
sizes = 1000 * rng.rand(12)

plt.scatter(x, y, colors=colors, s=sizes, alpha=0.3,
            cmap='viridis')
plt.colorbar();  # show color scale
plt.show()

[jklymak]

Did you try color Instead of colors?