scatter plot logarithmic scale

Question

In my code, I take the logarithm of two data series and plot them. I would like to change each tick value of the x-axis by raising it to the power of e (anti-log of natural logarithm).

In other words. I want to graph the logarithms of both series but have x-axis in levels.

enter image description here

Here is the code that I'm using.

from pylab import scatter
import pylab
import matplotlib.pyplot as plt
import pandas as pd
from pandas import Series, DataFrame
import numpy as np
file_name = '/Users/joedanger/Desktop/Python/scatter_python.csv'
data = DataFrame(pd.read_csv(file_name))
y = np.log(data['o_value'], dtype='float64')
x = np.log(data['time_diff_day'], dtype='float64')
fig = plt.figure()
plt.scatter(x, y, c='blue', alpha=0.05, edgecolors='none')
fig.suptitle('test title', fontsize=20)
plt.xlabel('time_diff_day', fontsize=18)
plt.ylabel('o_value', fontsize=16)
plt.xticks([-8,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4])
plt.grid(True)
pylab.show()

Answer 1

let matplotlib take the log for you:

fig = plt.figure()
ax = plt.gca()
ax.scatter(data['o_value'] ,data['time_diff_day'] , c='blue', alpha=0.05, edgecolors='none')
ax.set_yscale('log')
ax.set_xscale('log')

If you are using all the same size and color markers, it is faster to use plot

fig = plt.figure()
ax = plt.gca()
ax.plot(data['o_value'] ,data['time_diff_day'], 'o', c='blue', alpha=0.05, markeredgecolor='none')
ax.set_yscale('log')
ax.set_xscale('log')

• uhoh: @tcaswell I'm having trouble using plt.yscale('log') after a plt.scatter() and have described the problem in this question.
• Aviad Rozenhek: does ax.set_yscale('log') use np.log or np.log1p for the conversion?

Answer 2

The accepted answer is a bit out of date. At least pandas 0.25 natively supports log axes:

# logarithmic X
df.plot.scatter(..., logx=True)
# logarithmic Y
df.plot.scatter(..., logy=True)
# both
df.plot.scatter(..., loglog=True)

• user202729: It's not really correct to say the other answer is out of date. Note that the question asks for matplotlib which doesn't support logx=, while you're using pandas (which uses matplotlib under the hood, but still)
• Marat: @user202729 OP is clearly using Pandas ("two data series", code fragment). The accepted answer is not wrong, but there's a newer and better alternative, which dozens of people found helpful. IDK, sounds like out of date to me.