No color when I make python scatter color plot using third variable to define color

Question

I try to make colorful scatter plot using third variable to define color. It is simple to use the following code:

plt.scatter(mH, mA, s=1, c=mHc)
plt.colorbar()
plt.show()

But I do not have many choices to modify the frame of the plot. I am trying the following code to make colorful scatter plot, at the same time I try to optimize the frame of the plot:

import numpy as np
import math
from matplotlib import rcParams
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator

fig, ax = plt.subplots()

cax = ax.scatter(mH,mA,s=0.5,c=mHc) ### mH, mA, mHC are the dataset
fig.colorbar(cax)
minor_locator1 = AutoMinorLocator(6)
minor_locator2 = AutoMinorLocator(6)
ax.xaxis.set_minor_locator(minor_locator1)
ax.yaxis.set_minor_locator(minor_locator2)
ax.tick_params('both', length=10, width=2, which='major')
ax.tick_params('both', length=5, width=2, which='minor')
ax.set_xlabel(r'$m_H$')
ax.set_ylabel(r'$m_A$')
ax.set_xticks([300,600,900,1200,1500])
ax.set_yticks([300,600,900,1200,1500])

plt.savefig('mH_mA.png',bbox_inches='tight')
plt.show()

But the plot I got is black-white. It looks like the problem lies in the marker size argument, but I do not have much idea how to correct it. I want to have smaller marker size. Anyone can offer me some idea to approach this issue. Thanks.

ali_m · Accepted Answer · 2016-06-22 00:55:07Z

3

size=0.5 is extremely small - probably all you are seeing is the marker outlines. I would suggest you increase the size a bit, and perhaps pass edgecolors="none" to turn off the marker edge stroke:

import numpy as np
from matplotlib import pyplot as plt

n = 10000
x, y = np.random.randn(2, n)
z = -(x**2 + y**2)**0.5

fig, ax = plt.subplots(1, 1)
ax.scatter(x, y, s=5, c=z, cmap="jet", edgecolors="none")

You might also want to experiment with making the points semi-transparent using the alpha= parameter:

ax.scatter(x, y, s=20, c=z, alpha=0.1, cmap="jet", edgecolors="none")

It can be difficult to get scatter plots to look nice when you have such a massive number of overlapping points. I would be tempted to plot your data as a 2D histogram or contour plot instead, or perhaps even a combination of a scatter plot and a contour plot:

density, xe, ye = np.histogram2d(x, y, bins=20, normed=True)
ax.hold(True)
ax.scatter(x, y, s=5, c=z, cmap="jet", edgecolors="none")
ax.contour(0.5*(xe[:-1] + xe[1:]), 0.5*(ye[:-1] + ye[1:]), density,
           colors='k')

answered Jun 22, 2016 at 0:55

ali_m

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1 Comment

Huanian Zhang Over a year ago

Thanks a lot. It is so helpful.

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