plotting both x and y axis in log scale in pandas

Question:

Everything is fine when I plot only y axis in log scale.

import pandas as pd
import numpy
import matplotlib.pyplot as plt

iplevel = pd.read_csv('iplevel.csv')
fig = plt.figure()
#plt.xscale('log')
plt.yscale('log')
plt.title(' Size Vs Duration (at IP level) for ')

plt.xlabel('Duration (in seconds)')
plt.ylabel('Size (in bytes)')
plt.scatter(iplevel['Time'], iplevel['Length'])
fig.tight_layout()
fig.savefig('iplevel_timevdur.png', dpi=fig.dpi)

Only y axis in log scale

Something strange happens when I plot both x and y axis in log scale.

iplevel = pd.read_csv('iplevel.csv')
fig = plt.figure()
plt.xscale('log')
plt.yscale('log')
plt.title(' Size Vs Duration (at IP level) for ')

plt.xlabel('Duration (in seconds)')
plt.ylabel('Size (in bytes)')
plt.scatter(iplevel['Time'], iplevel['Length'])
fig.tight_layout()
fig.savefig('iplevel_timevdur.png', dpi=fig.dpi)

enter image description here

I am not sure where I am going wrong. Any ideas/suggestions welcome

My trace file can be downloaded from here. Here are the top 1800 of 2715 rows sorted by 'Time'.

Length,Time
64,0.0
64,0.0
64,0.0
863,0.0
259,0.0
64,0.0
64,0.0
78,0.0
64,0.0
64,0.0
64,0.0
86,0.0
64,0.0
102,0.0
64,0.0
140,0.0
90,0.0
140,0.0
152,0.0
260,0.0
64,0.0
1419,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
140,0.0
64,0.0
140,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
634,0.0
64,0.0
64,0.0
64,0.0
64,0.0
78,0.0
64,0.0
1241,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
66,0.0
64,0.0
64,0.0
64,0.0
66,0.0
66,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
78,0.0
66,0.0
66,0.0
66,0.0
64,0.0
66,0.0
66,0.0
64,0.0
64,0.0
64,0.0
140,0.0
140,0.0
140,0.0
66,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
70,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
64,0.0
70,0.0
64,0.0
64,0.0
64,0.0
70,0.0
64,0.0
82,0.0
70,0.0
122,0.0
70,0.0
174,0.0
64,0.0
911,0.0
64,0.0
64,0.0
64,0.0
128,0.0
129,0.0
64,0.0
64,0.0
140,0.0
140,0.0
64,0.0
94,0.0
1518,0.0
64,0.0
64,0.0
68,0.0
127,0.0
70,0.0
86,0.0
66,0.0
66,0.0
64,0.0
66,0.0
66,0.0
66,0.0
64,0.0
70,0.0
86,0.0
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66,0.0
64,0.0
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64,0.0
140,0.0
1045,0.0
64,0.0
70,0.0
64,0.0
64,0.0
70,0.0
64,0.0
140,0.0
66,0.0
70,0.0
140,0.0
64,0.0
64,0.0
171,0.0
128,4.00000000411e-06
128,4.99999999803e-06
128,8.00000000112e-06
128,2.29999999988e-05
448,3.00000000002e-05
140,4.40000000026e-05
256,7.19999999959e-05
384,0.000106999999986
320,0.000121000000007
384,0.000253999999984
128,0.000342
204,0.000381000000004
140,0.000453
204,0.000878999999998
358,0.001082
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174,0.00224799999998
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635,0.00283899999997
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128,0.00412900000001
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128,0.00425200000001
128,0.00436499999995
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128,0.00491100000001
128,0.00500199999999
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1128,0.00558500000001
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128,0.00665499999999
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1920,0.050076
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2613,0.0541250000001
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401,0.065523
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1835,0.07433
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5808,0.07657
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192,0.079372
740,0.079504
1017,0.083836
357,0.084731
1311,0.084966
646,0.085513
382,0.085933
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64438,0.097073
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1085,0.104543
1707,0.106295
128,0.107193
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1024,91.274712
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Asked By: user2532296

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Answers:

It looks like you have some zeros in your X values. log(0) isn’t defined, log(veryclosetozero) is 10^{-verymuch}.

Edit:
In addition, float representation of numbers isn’t always completely exact, so 0.0 might end up being stored as 0.00000000000000000001 or similar. The log function would not throw an error in that case, but simply calculate the logarithm of something very very small.

Answered By: Alex

I faced a similar problem when plotting numbers containing a lot of zeros. If your number is represented like 10E-38 format in the csv file, try multiplying all the rows by 1 and then read the data using pandas.

This solved the problem in my case.

Answered By: Stoner
import pandas as pd

# path to data from the link in the OP
data_path = 'https://gist.githubusercontent.com/ecenm/25df526d4398af2c3e41ae6df6c51155/raw/a6a72e4ed46604b019bb14a275044aff829fb2bc/iplevel.csv'
df = pd.read_csv(data_path)

# understand the distribution
display(df.describe())
  • See that 'Length' has a wide distribution with large standard deviation and variance df.Length.var() → 2565470083120.9233
             Length         Time
count  2.715000e+03  2715.000000
mean   1.748645e+05    94.257661
std    1.601708e+06   117.789762
min    6.400000e+01     0.000000
25%    6.290000e+02     0.659420
50%    4.396000e+03    25.368997
75%    3.863800e+04   182.597445
max    7.349447e+07   344.968822
ax = df.plot(kind='box', column='Length', figsize=(12, 6), grid=False, logy='sym')

enter image description here

ax = df.plot(kind='box', column='Time', figsize=(12, 6), grid=False, logy='sym')

enter image description here

  • Use pandas.DataFrame.plot with logy=True, or logy='sym'
ax = df.plot(kind='scatter', x='Time', y='Length', logy=True, figsize=(10, 7), s=1,
             xlabel='Duration (in seconds)', ylabel='Size (in bytes)', title='Size Vs Duration (at IP level)')

enter image description here

  • Use pandas.DataFrame.plot with logy=True and logx=True
ax = df.plot(kind='scatter', x='Time', y='Length', logx=True, logy=True, figsize=(10, 7),
             xlabel='Duration (in seconds)', ylabel='Size (in bytes)', title='Size Vs Duration (at IP level)')

enter image description here

  • Use pandas.DataFrame.plot with logx='sym' and logy='sym'
ax = df.plot(kind='scatter', x='Time', y='Length', logx='sym', logy='sym', figsize=(10, 7), s=1,
             xlabel='Duration (in seconds)', ylabel='Size (in bytes)', title='Size Vs Duration (at IP level)')

enter image description here


  • Plots with the original code from the OP

enter image description here

enter image description here

Answered By: Trenton McKinney
Categories: questions Tags: , ,
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