CODEWITHSUNDEEP
pythonnumpymatplotlibpandasregression
TimStuart
TimStuart

Reputation: 434

Linear regression with pandas dataframe

I have a dataframe in pandas that I'm using to produce a scatterplot, and want to include a regression line for the plot. Right now I'm trying to do this with polyfit.

Here's my code:

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

table1 = pd.DataFrame.from_csv('upregulated_genes.txt', sep='\t', header=0, index_col=0)
table2 = pd.DataFrame.from_csv('misson_genes.txt', sep='\t', header=0, index_col=0)
table1 = table1.join(table2, how='outer')

table1 = table1.dropna(how='any')
table1 = table1.replace('#DIV/0!', 0)

# scatterplot
plt.scatter(table1['log2 fold change misson'], table1['log2 fold change'])
plt.ylabel('log2 expression fold change')
plt.xlabel('log2 expression fold change Misson et al. 2005')
plt.title('Root Early Upregulated Genes')
plt.axis([0,12,-5,12])

# this is the part I'm unsure about
regres = polyfit(table1['log2 fold change misson'], table1['log2 fold change'], 1)

plt.show()

But I get the following error:

TypeError: cannot concatenate 'str' and 'float' objects

Does anyone know where I'm going wrong here? I'm also unsure how to add the regression line to my plot. Any other general comments on my code would also be hugely appreciated, I'm still a beginner.

Upvotes: 14

Views: 30279

Answers (1)

Dan Allan
Dan Allan

Reputation: 35235

Instead of replacing '#DIV/0!' by hand, force the data to be numeric. This does two things at once: it ensures that the result is numeric type (not str), and it substitutes NaN for any entries that cannot be parsed as a number. Example:

In [5]: Series([1, 2, 'blah', '#DIV/0!']).convert_objects(convert_numeric=True)
Out[5]: 
0     1
1     2
2   NaN
3   NaN
dtype: float64

This should fix your error. But, on the general subject of fitting a line to data, I keep handy two ways of doing this that I like better than polyfit. The second of the two is more robust (and can potentially return much more detailed information about the statistics) but it requires statsmodels.

from scipy.stats import linregress
def fit_line1(x, y):
    """Return slope, intercept of best fit line."""
    # Remove entries where either x or y is NaN.
    clean_data = pd.concat([x, y], 1).dropna(0) # row-wise
    (_, x), (_, y) = clean_data.iteritems()
    slope, intercept, r, p, stderr = linregress(x, y)
    return slope, intercept # could also return stderr

import statsmodels.api as sm
def fit_line2(x, y):
    """Return slope, intercept of best fit line."""
    X = sm.add_constant(x)
    model = sm.OLS(y, X, missing='drop') # ignores entires where x or y is NaN
    fit = model.fit()
    return fit.params[1], fit.params[0] # could also return stderr in each via fit.bse

To plot it, do something like

m, b = fit_line2(x, y)
N = 100 # could be just 2 if you are only drawing a straight line...
points = np.linspace(x.min(), x.max(), N)
plt.plot(points, m*points + b)

Upvotes: 28

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