Pandas matrix confusion with plot features (matplotlib, seaborn...)
Project description
pandas_confusion
A Python Pandas implementation of confusion matrix.
WORK IN PROGRESS - Use it a your own risk
Usage
Confusion matrix
Import ConfusionMatrix
from pandas_confusion import ConfusionMatrix
Define actual values (y_actu) and predicted values (y_pred)
y_actu = ['rabbit', 'cat', 'rabbit', 'rabbit', 'cat', 'dog', 'dog', 'rabbit', 'rabbit', 'cat', 'dog', 'rabbit'] y_pred = ['cat', 'cat', 'rabbit', 'dog', 'cat', 'rabbit', 'dog', 'cat', 'rabbit', 'cat', 'rabbit', 'rabbit']
Let’s define a (non binary) confusion matrix
confusion_matrix = ConfusionMatrix(y_actu, y_pred)
print("Confusion matrix:\n%s" % confusion_matrix)
You can see it
Predicted cat dog rabbit __all__ Actual cat 3 0 0 3 dog 0 1 2 3 rabbit 2 1 3 6 __all__ 5 2 5 12
Matplotlib plot of a confusion matrix
Inside a IPython notebook add this line as first cell
%matplotlib inline
You can plot confusion matrix using:
import matplotlib.pyplot as plt confusion_matrix.plot()
If you are not using inline mode, you need to use to show confusion matrix plot.
plt.show()
confusion_matrix
Matplotlib plot of a normalized confusion matrix
confusion_matrix.plot(normalized=True) plt.show()
confusion_matrix_norm
Binary confusion matrix
Import BinaryConfusionMatrix and Backend
from pandas_confusion import BinaryConfusionMatrix, Backend
Define actual values (y_actu) and predicted values (y_pred)
y_actu = [ True, True, False, False, False, True, False, True, True,
False, True, False, False, False, False, False, True, False,
True, True, True, True, False, False, False, True, False,
True, False, False, False, False, True, True, False, False,
False, True, True, True, True, False, False, False, False,
True, False, False, False, False, False, False, False, False,
False, True, True, False, True, False, True, True, True,
False, False, True, False, True, False, False, True, False,
False, False, False, False, False, False, False, True, False,
True, True, True, True, False, False, True, False, True,
True, False, True, False, True, False, False, True, True,
False, False, True, True, False, False, False, False, False,
False, True, True, False]
y_pred = [False, False, False, False, False, True, False, False, True,
False, True, False, False, False, False, False, False, False,
True, True, True, True, False, False, False, False, False,
False, False, False, False, False, True, False, False, False,
False, True, False, False, False, False, False, False, False,
True, False, False, False, False, False, False, False, False,
False, True, False, False, False, False, False, False, False,
False, False, True, False, False, False, False, True, False,
False, False, False, False, False, False, False, True, False,
False, True, False, False, False, False, True, False, True,
True, False, False, False, True, False, False, True, True,
False, False, True, True, False, False, False, False, False,
False, True, False, False]
Let’s define a binary confusion matrix
binary_confusion_matrix = BinaryConfusionMatrix(y_actu, y_pred)
print("Binary confusion matrix:\n%s" % binary_confusion_matrix)
It display as a nicely labeled Pandas DataFrame
Binary confusion matrix: Predicted False True __all__ Actual False 67 0 67 True 21 24 45 __all__ 88 24 112
You can get useful attributes such as True Positive (TP), True Negative (TN) …
print binary_confusion_matrix.TP
Matplotlib plot of a binary confusion matrix
binary_confusion_matrix.plot() plt.show()
binary_confusion_matrix
Matplotlib plot of a normalized binary confusion matrix
binary_confusion_matrix.plot(normalized=True) plt.show()
binary_confusion_matrix_norm
Seaborn plot of a binary confusion matrix (ToDo)
from pandas_confusion import Backend binary_confusion_matrix.plot(backend=Backend.Seaborn)
Confusion matrix and class statistics
Overall statistics and class statistics of confusion matrix can be easily displayed.
y_true = [600, 200, 200, 200, 200, 200, 200, 200, 500, 500, 500, 200, 200, 200, 200, 200, 200, 200, 200, 200] y_pred = [100, 200, 200, 100, 100, 200, 200, 200, 100, 200, 500, 100, 100, 100, 100, 100, 100, 100, 500, 200] cm = ConfusionMatrix(y_true, y_pred) cm.print_stats()
You should get:
Confusion Matrix: Classes 100 200 500 600 __all__ Actual 100 0 0 0 0 0 200 9 6 1 0 16 500 1 1 1 0 3 600 1 0 0 0 1 __all__ 11 7 2 0 20 Overall Statistics: Accuracy: 0.35 95% CI: (0.1539092047845412, 0.59218853453282805) No Information Rate: ToDo P-Value [Acc > NIR]: 0.978585644357 Kappa: 0.0780141843972 Mcnemar's Test P-Value: ToDo Class Statistics: Classes 100 200 500 600 Population 20 20 20 20 Condition positive 0 16 3 1 Condition negative 20 4 17 19 Test outcome positive 11 7 2 0 Test outcome negative 9 13 18 20 TP: True Positive 0 6 1 0 TN: True Negative 9 3 16 19 FP: False Positive 11 1 1 0 FN: False Negative 0 10 2 1 TPR: Sensivity NaN 0.375 0.3333333 0 TNR=SPC: Specificity 0.45 0.75 0.9411765 1 PPV: Pos Pred Value = Precision 0 0.8571429 0.5 NaN NPV: Neg Pred Value 1 0.2307692 0.8888889 0.95 FPR: False-out 0.55 0.25 0.05882353 0 FDR: False Discovery Rate 1 0.1428571 0.5 NaN FNR: Miss Rate NaN 0.625 0.6666667 1 ACC: Accuracy 0.45 0.45 0.85 0.95 F1 score 0 0.5217391 0.4 0 MCC: Matthews correlation coefficient NaN 0.1048285 0.326732 NaN Informedness NaN 0.125 0.2745098 0 Markedness 0 0.08791209 0.3888889 NaN Prevalence 0 0.8 0.15 0.05 LR+: Positive likelihood ratio NaN 1.5 5.666667 NaN LR-: Negative likelihood ratio NaN 0.8333333 0.7083333 1 DOR: Diagnostic odds ratio NaN 1.8 8 NaN FOR: False omission rate 0 0.7692308 0.1111111 0.05
Statistics are also available as an OrderedDict using:
cm.stats()
Install
$ conda install pandas scikit-learn scipy $ pip install pandas_confusion
Development
You can help to develop this library.
Issues
You can submit issues using https://github.com/scls19fr/pandas_confusion/issues
Clone
You can clone repository to try to fix issues yourself using:
$ git clone https://github.com/scls19fr/pandas_confusion.git
Run unit tests
Run all unit tests
$ nosetests -s -v
Run a given test
$ nosetests -s -v tests/test_pandas_confusion.py:test_pandas_confusion_normalized
Install development version
$ python setup.py install
or
$ sudo pip install git+git://github.com/scls19fr/pandas_confusion.git
Collaborating
Fork repository
Create a branch which fix a given issue
Submit pull requests
Done
Continuous integration (Travis)
Convert a confusion matrix to a binary confusion matrix
Python package
Unit tests (nose)
Fix missing column and missing row
Overall statistics: Accuracy, 95% CI, P-Value [Acc > NIR], Kappa
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