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I have created logistic regression model with my X_variable being income and y variable being a binary variable of whether the business accepts card or cash (link to data at the end), I used sklearn python library to do so and these are the charts I got:

enter image description here

However the issue is that while the chart on the right makes sense, with the chart on the left I would expect the line to have negative coefficient as the scatter plot suggest, the y values of value 0 are in the region where the net annual income is higher. Furthermore, I ran the regression using statsmodel library (very similar to R programming language) where I got a full summary and there the coefficient for cash is negative while for card positive (as I would expect it to be)

enter image description here

The data that I used: https://pastebin.com/ShPxuqmL

Example code:

import matplotlib as plt
from sklearn.linear_model import LogisticRegression


clf = LogisticRegression()
clf.fit(X, y)
plt.scatter(X_train, y_train)
x_range = np.linspace(X.min(), X.max(), 100)
y_range = clf.predict_proba(X.reshape(-1,1))[:,1]
plt.plot(X, y, color='red',label='logistic line')
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    $\begingroup$ Yes, the plot for the second output should depict an increasing line. But the linked data only contains one binary $y$, has a different sample size ($208$) than either of the shown outputs and I cannot replicate either model with it in R: My coefficients are $5.86265$ and $-0.0001057$. So what exactly did you do and what data did you actually use? How did you create the plots? $\endgroup$
    – COOLSerdash
    Feb 26 at 14:21
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    $\begingroup$ The detail in the plots is inadequate even for estimating the sign of the slope. One effective way to draw such plots is to jitter the heights of the points a little so you can see (roughly) their density. $\endgroup$
    – whuber ♦
    Feb 26 at 14:30
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    $\begingroup$ Thanks but we still don't know how the plots were produced. All we know is that they don't correspond to any of the two outputs. $\endgroup$
    – COOLSerdash
    Feb 26 at 14:41
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    $\begingroup$ By default, Sklearn applies a penalty to logistic regression coefficient estimates. This is stated in the sklearn documentation. Perhaps this is why the sklearn and statsmodels outputs are different. See: stats.stackexchange.com/questions/203740/… $\endgroup$
    – Sycorax ♦
    Feb 26 at 17:00
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    $\begingroup$ I think the duplicate addresses at least nearly all of this question. If you disagree, you'll need to edit to create a minimal, reproducible example (including data) so that other people can reproduce and diagnose the behavior. $\endgroup$
    – Sycorax ♦
    Feb 27 at 16:23

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