Type error: plotting linear regression

Question

New to Python, trying to plot linear regression of two lists. This is what I have so far:

#!/usr/bin/python

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from numpy import arange,array,ones#,random,linalg
from pylab import plot,show
from scipy import stats
from sys import argv

a = argv[1]
b = argv[2]

list1 = open(a)
list2 = open(b)

xi = list1.read().splitlines()
y = list2.read().splitlines()

slope, intercept, r_value, p_value, std_err = stats.linregress(xi,y)

print 'r value', r_value

line = slope*xi+intercept
plot(xi,line,'r-',xi,y,'o')
plt.savefig('myfig')

I get the following error:

Traceback (most recent call last):
  File "plot.py", line 21, in <module>
    slope, intercept, r_value, p_value, std_err = stats.linregress(xi,y)
  File "/export/apps/Python/2.7.2-CentOS6.0/lib/python2.7/site-packages/scipy/stats/stats.py", line 3007, in linregress                                                                                         
    xmean = np.mean(x,None)                                                                             
  File "/export/apps/Python/2.7.2-CentOS6.0/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2727, in mean                                                                                          
    out=out, keepdims=keepdims)                                                                         
  File "/export/apps/Python/2.7.2-CentOS6.0/lib/python2.7/site-packages/numpy/core/_methods.py", line 66, in _mean                                                                                              
    ret = umr_sum(arr, axis, dtype, out, keepdims)                                                      
TypeError: cannot perform reduce with flexible type

Brionius · Accepted Answer · 2015-02-25 17:04:06Z

1

My guess would be that it's not kosher to pass in a list of strings to linregress. Try converting them to floats first:

xi = [float(xk) for xk in xi]
y = [float(yk) for yk in y]
slope, intercept, r_value, p_value, std_err = stats.linregress(xi,y)

Depending on what's in xi and y, you might have to strip some empty strings first, or otherwise sanitize the input.

answered Feb 25, 2015 at 17:04

Brionius

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1 Comment

EA00 Over a year ago

thanks, it worked! I also had to clear empty strings like you mentioned.

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