How to use different marker for different point in scatter plot pylab

Question

I want to use the scatter plot function of pylab

x = [1,2,3,4,5]
y = [2,1,3,6,7]

there are two clusters in this 5 points, index 1-2(cluster 1) and index 2-4 (cluster 2). The point in cluster 1 should use marker '^', whereas the point in cluster 2 should use marker 's'. so

cluster = ['^','^','^','s','s']

I have tried

fig, ax = pl.subplots()
ax.scatter(x,y,marker=cluster)
pl.show()

This is a toy example, real data have more than 10000 samples

Answer 1

To achieve this result you need to call scatter multiple times on the same axis. The good news is you can automate this for your given data:

import matplotlib.pyplot as plt

x = [1,2,3,4,5]
y = [2,1,3,6,7]

cluster = ['^','^','^','s','s']

fig, ax = plt.subplots()

for xp, yp, m in zip(x, y, cluster):
    ax.scatter([xp],[yp], marker=m)

plt.show()

A neater solution would be to filter your input data using your cluster information. We can do that using numpy.

import matplotlib.pyplot as plt
import numpy as np

x = np.array([1,2,3,4,5])
y = np.array([2,1,3,6,7])

cluster = np.array([1,1,1,2,2]) 

fig, ax = plt.subplots()

ax.scatter(x[cluster==1],y[cluster==1], marker='^')
ax.scatter(x[cluster==2],y[cluster==2], marker='s')

plt.show()