I am trying to make a scatter plot and annotate data points with different numbers from a list. So, for example, I want to plot y vs x and annotate with corresponding numbers from n.

y = [2.56422, 3.77284, 3.52623, 3.51468, 3.02199]
z = [0.15, 0.3, 0.45, 0.6, 0.75]
n = [58, 651, 393, 203, 123]
ax = fig.add_subplot(111)
ax1.scatter(z, y, fmt='o')

Any ideas?

I’m not aware of any plotting method which takes arrays or lists but you could use annotate() while iterating over the values in n.

y = [2.56422, 3.77284, 3.52623, 3.51468, 3.02199]
z = [0.15, 0.3, 0.45, 0.6, 0.75]
n = [58, 651, 393, 203, 123]

fig, ax = plt.subplots()
ax.scatter(z, y)

for i, txt in enumerate(n):
    ax.annotate(txt, (z[i], y[i]))

There are a lot of formatting options for annotate(), see the matplotlib website:

In version’s earlier than matplotlib 2.0, ax.scatter is not necessary to plot text without markers. In version 2.0 you’ll need ax.scatter to set the proper range and markers for text.

y = [2.56422, 3.77284, 3.52623, 3.51468, 3.02199]
z = [0.15, 0.3, 0.45, 0.6, 0.75]
n = [58, 651, 393, 203, 123]

fig, ax = plt.subplots()

for i, txt in enumerate(n):
    ax.annotate(txt, (z[i], y[i]))

And in this link you can find an example in 3d.

In case anyone is trying to apply the above solutions to a .scatter() instead of a .subplot(),

I tried running the following code

y = [2.56422, 3.77284, 3.52623, 3.51468, 3.02199]
z = [0.15, 0.3, 0.45, 0.6, 0.75]
n = [58, 651, 393, 203, 123]

fig, ax = plt.scatter(z, y)

for i, txt in enumerate(n):
    ax.annotate(txt, (z[i], y[i]))

But ran into errors stating “cannot unpack non-iterable PathCollection object”, with the error specifically pointing at codeline fig, ax = plt.scatter(z, y)

I eventually solved the error using the following code

plt.scatter(z, y)

for i, txt in enumerate(n):
    plt.annotate(txt, (z[i], y[i]))

I didn’t expect there to be a difference between .scatter() and .subplot() I should have known better.

You may also use pyplot.text (see here).

def plot_embeddings(M_reduced, word2Ind, words):
    """ 
        Plot in a scatterplot the embeddings of the words specified in the list "words".
        Include a label next to each point.
    """
    for word in words:
        x, y = M_reduced[word2Ind[word]]
        plt.scatter(x, y, marker='x', color='red')
        plt.text(x+.03, y+.03, word, fontsize=9)
    plt.show()

M_reduced_plot_test = np.array([[1, 1], [-1, -1], [1, -1], [-1, 1], [0, 0]])
word2Ind_plot_test = {'test1': 0, 'test2': 1, 'test3': 2, 'test4': 3, 'test5': 4}
words = ['test1', 'test2', 'test3', 'test4', 'test5']
plot_embeddings(M_reduced_plot_test, word2Ind_plot_test, words)

Python 3.6+:

coordinates = [('a',1,2), ('b',3,4), ('c',5,6)]
for x in coordinates: plt.annotate(x[0], (x[1], x[2]))

As a one liner using list comprehension and numpy:

[ax.annotate(x[0], (x[1], x[2])) for x in np.array([n,z,y]).T]

setup is ditto to Rutger’s answer.

I would love to add that you can even use arrows /text boxes to annotate the labels. Here is what I mean:

import random
import matplotlib.pyplot as plt


y = [2.56422, 3.77284, 3.52623, 3.51468, 3.02199]
z = [0.15, 0.3, 0.45, 0.6, 0.75]
n = [58, 651, 393, 203, 123]

fig, ax = plt.subplots()
ax.scatter(z, y)

ax.annotate(n[0], (z[0], y[0]), xytext=(z[0]+0.05, y[0]+0.3), 
    arrowprops=dict(facecolor='red', shrink=0.05))

ax.annotate(n[1], (z[1], y[1]), xytext=(z[1]-0.05, y[1]-0.3), 
    arrowprops = dict(  arrowstyle="->",
                        connectionstyle="angle3,angleA=0,angleB=-90"))

ax.annotate(n[2], (z[2], y[2]), xytext=(z[2]-0.05, y[2]-0.3), 
    arrowprops = dict(arrowstyle="wedge,tail_width=0.5", alpha=0.1))

ax.annotate(n[3], (z[3], y[3]), xytext=(z[3]+0.05, y[3]-0.2), 
    arrowprops = dict(arrowstyle="fancy"))

ax.annotate(n[4], (z[4], y[4]), xytext=(z[4]-0.1, y[4]-0.2),
    bbox=dict(boxstyle="round", alpha=0.1), 
    arrowprops = dict(arrowstyle="simple"))

plt.show()

Which will generate the following graph: