Python – Generate a heatmap in MatPlotLib using a scatter data set

heatmaphistogram2dmatplotlibpython

I have a set of X,Y data points (about 10k) that are easy to plot as a scatter plot but that I would like to represent as a heatmap.

I looked through the examples in MatPlotLib and they all seem to already start with heatmap cell values to generate the image.

Is there a method that converts a bunch of x,y, all different, to a heatmap (where zones with higher frequency of x,y would be "warmer")?

Best Answer

If you don't want hexagons, you can use numpy's histogram2d function:

import numpy as np
import numpy.random
import matplotlib.pyplot as plt

# Generate some test data
x = np.random.randn(8873)
y = np.random.randn(8873)

heatmap, xedges, yedges = np.histogram2d(x, y, bins=50)
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]

plt.clf()
plt.imshow(heatmap.T, extent=extent, origin='lower')
plt.show()

This makes a 50x50 heatmap. If you want, say, 512x384, you can put bins=(512, 384) in the call to histogram2d.

Example: Matplotlib heat map example

Related Solutions

Python – Generate a heatmap in MatPlotLib using a scatter data set

Convert your time series data into a numeric format with matplotlib.dats.date2num. Lay down a rectangular grid that spans your x and y ranges and do your convolution on that plot. Make a pseudo-color plot of your convolution and then reformat the x labels to be dates.

The label formatting is a little messy, but reasonably well documented. You just need to replace AutoDateFormatter with DateFormatter and an appropriate formatting string.

You'll need to tweak the constants in the convolution for your data.

import numpy as np
import datetime as dt
import pylab as plt
import matplotlib.dates as dates

t0 = dt.date.today()
t1 = t0+dt.timedelta(days=10)

times = np.linspace(dates.date2num(t0), dates.date2num(t1), 10)
dt = times[-1]-times[0]
price =  100 - (times-times.mean())**2
dp = price.max() - price.min()
volume = np.linspace(1, 100, 10)

tgrid = np.linspace(times.min(), times.max(), 100)
pgrid = np.linspace(70, 110, 100)
tgrid, pgrid = np.meshgrid(tgrid, pgrid)
heat = np.zeros_like(tgrid)

for t,p,v in zip(times, price, volume):
    delt = (t-tgrid)**2
    delp = (p-pgrid)**2
    heat += v/( delt + delp*1.e-2 + 5.e-1 )**2

fig = plt.figure()
ax = fig.add_subplot(111)
ax.pcolormesh(tgrid, pgrid, heat, cmap='gist_heat_r')

plt.scatter(times, price, volume, marker='x')

locator = dates.DayLocator()
ax.xaxis.set_major_locator(locator)
ax.xaxis.set_major_formatter(dates.AutoDateFormatter(locator))
fig.autofmt_xdate()

plt.show()

Script output

Python – Save plot to image file instead of displaying it using Matplotlib

While the question has been answered, I'd like to add some useful tips when using matplotlib.pyplot.savefig. The file format can be specified by the extension:

from matplotlib import pyplot as plt

plt.savefig('foo.png')
plt.savefig('foo.pdf')

Will give a rasterized or vectorized output respectively, both which could be useful. In addition, there's often an undesirable, whitespace around the image, which can be removed with:

plt.savefig('foo.png', bbox_inches='tight')

Note that if showing the plot, plt.show() should follow plt.savefig(), otherwise the file image will be blank.

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Related Solutions

Python – Generate a heatmap in MatPlotLib using a scatter data set

Python – Save plot to image file instead of displaying it using Matplotlib

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