# This Python 3 environment comes with many helpful analytics libraries installed

# It is defined by the kaggle/python Docker image:

https://github.com/kaggle/docker-python
# For example, here's several helpful packages to load

import numpy as np # linear algebra

import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)
import seaborn as sns
import matplotlib.pyplot as plot
from scipy import stats
plot.style.use("ggplot")
import warnings
warnings.filterwarnings("ignore")
from scipy import stats

# Input data files are available in the read-only "../input/" directory

# For example, running this (by clicking run or pressing Shift+Enter) will list all
files under the input directory

import os
for dirname, _, filenames in os.walk('/kaggle/input'):
for filename in filenames:
print(os.path.join(dirname, filename))

# You can write up to 20GB to the current directory (/kaggle/working/) that gets
preserved as output when you create a version using "Save & Run All"
# You can also write temporary files to /kaggle/temp/, but they won't be saved
outside of the current session
/kaggle/input/breast-cancer-wisconsin-data/data.csv
Load data
data = pd.read_csv("../input/breast-cancer-wisconsin-data/data.csv")
data.head()
id diagnosis radius_mean texture_mean perimeter_mean area_mean
smoothness_mean compactness_mean concavity_mean concave points_mean
... texture_worst perimeter_worst area_worst smoothness_worst
compactness_worst concavity_worst concave points_worst symmetry_worst
fractal_dimension_worst Unnamed: 32
0 842302 M 17.99 10.38 122.80 1001.0 0.11840 0.27760
0.3001 0.14710 ... 17.33 184.60 2019.0 0.1622 0.6656
0.7119 0.2654 0.4601 0.11890 NaN
1 842517 M 20.57 17.77 132.90 1326.0 0.08474 0.07864
0.0869 0.07017 ... 23.41 158.80 1956.0 0.1238 0.1866
0.2416 0.1860 0.2750 0.08902 NaN
2 84300903 M 19.69 21.25 130.00 1203.0 0.10960 0.15990
0.1974 0.12790 ... 25.53 152.50 1709.0 0.1444 0.4245
0.4504 0.2430 0.3613 0.08758 NaN
3 84348301 M 11.42 20.38 77.58 386.1 0.14250 0.28390 0.2414
0.10520 ... 26.50 98.87 567.7 0.2098 0.8663 0.6869 0.2575
0.6638 0.17300 NaN
4 84358402 M 20.29 14.34 135.10 1297.0 0.10030 0.13280
0.1980 0.10430 ... 16.67 152.20 1575.0 0.1374 0.2050
0.4000 0.1625 0.2364 0.07678 NaN
5 rows × 33 columns

data = data.drop(['Unnamed: 32','id'],axis=1)

data.head()
diagnosis radius_mean texture_mean perimeter_mean area_mean
smoothness_mean compactness_mean concavity_mean concave points_mean
symmetry_mean ... radius_worst texture_worst perimeter_worst
 area_worst smoothness_worst compactness_worst concavity_worst concave
points_worst symmetry_worst fractal_dimension_worst
0 M 17.99 10.38 122.80 1001.0 0.11840 0.27760 0.3001
0.14710 0.2419 ... 25.38 17.33 184.60 2019.0 0.1622
0.6656 0.7119 0.2654 0.4601 0.11890
1 M 20.57 17.77 132.90 1326.0 0.08474 0.07864 0.0869
0.07017 0.1812 ... 24.99 23.41 158.80 1956.0 0.1238
0.1866 0.2416 0.1860 0.2750 0.08902
2 M 19.69 21.25 130.00 1203.0 0.10960 0.15990 0.1974
0.12790 0.2069 ... 23.57 25.53 152.50 1709.0 0.1444
0.4245 0.4504 0.2430 0.3613 0.08758
3 M 11.42 20.38 77.58 386.1 0.14250 0.28390 0.2414 0.10520
0.2597 ... 14.91 26.50 98.87 567.7 0.2098 0.8663 0.6869
0.2575 0.6638 0.17300
4 M 20.29 14.34 135.10 1297.0 0.10030 0.13280 0.1980
0.10430 0.1809 ... 22.54 16.67 152.20 1575.0 0.1374
0.2050 0.4000 0.1625 0.2364 0.07678
5 rows × 31 columns

data.shape
(569, 31)
data.columns
Index(['diagnosis', 'radius_mean', 'texture_mean', 'perimeter_mean',
'area_mean', 'smoothness_mean', 'compactness_mean', 'concavity_mean',
'concave points_mean', 'symmetry_mean', 'fractal_dimension_mean',
'radius_se', 'texture_se', 'perimeter_se', 'area_se', 'smoothness_se',
'compactness_se', 'concavity_se', 'concave points_se', 'symmetry_se',
'fractal_dimension_se', 'radius_worst', 'texture_worst',
'perimeter_worst', 'area_worst', 'smoothness_worst',
'compactness_worst', 'concavity_worst', 'concave points_worst',
'symmetry_worst', 'fractal_dimension_worst'],
dtype='object')
Histogram
m = plot.hist(data[data["diagnosis"] == "M"].radius_mean,bins=30,fc=(1,0,0,0.5),
label="Malignant")
b = plot.hist(data[data["diagnosis"] == "B"].radius_mean,bins=30,fc=(0,1,0,0.5),
label="Bening")
plot.legend()
plot.xlabel("Radius Mean Values")
plot.ylabel("Frequency")
plot.title("Histogram")
plot.show()

np.mean(data[data["diagnosis"] == "M"].radius_mean)
17.46283018867925
np.mean(data[data["diagnosis"] == "B"].radius_mean)
12.14652380952381
Box plot
melted_data = pd.melt(data,id_vars = "diagnosis", value_vars = ['radius_mean',
'texture_mean'])
sns.boxplot(x = "variable", y="value",hue="diagnosis", data=melted_data)
plot.show()

data_bening = data[data["diagnosis"] == "B"]

print("mean: ", data_bening.radius_mean.mean())
print("variance: ", data_bening.radius_mean.var())
print("std: ", data_bening.radius_mean.std())
print("median: ", data_bening.radius_mean.median(), "\n")
print("describe method: ", data_bening.radius_mean.describe())
mean: 12.14652380952381
variance: 3.170221722043872
std: 1.7805116461410389
median: 12.2

describe method: count 357.000000

mean 12.146524
std 1.780512
min 6.981000
25% 11.080000
50% 12.200000
75% 13.370000
max 17.850000
Name: radius_mean, dtype: float64
CDF (Cumulative distribution function)
CDF is the probability that the variable takes a value less than or equal to x. P(
plot.hist(data_bening.radius_mean, bins=50, fc=(0,1,0,0.5), label='bening',
cumulative = True)
# Why is this not possible to use 'normed = True' ?
sorted_data = np.sort(data_bening.radius_mean)
y = np.arange(len(sorted_data))/float(len(sorted_data)-1)
plot.plot(sorted_data,y,color='r')
plot.title('cdf')
plot.show()

sns.jointplot(data.radius_mean,data.area_mean,kind = "reg")
plot.show
<function matplotlib.pyplot.show(close=None, block=None)>

sns.set(style = "white")
df = data.loc[:,["radius_mean","area_mean","fractal_dimension_se"]]
g = sns.PairGrid(df,diag_sharey = False)
g.map_lower(sns.kdeplot, camp="Blues_d")
g.map_upper(plot.scatter)
g.map_diag(sns.kdeplot, lw = 3)
plot.show()

Correlation
f, ax = plot.subplots(figsize = (18,18))
sns.heatmap(data.corr(), annot = True, linewidths = 0.5, fmt = ".1f", ax = ax)
plot.xticks(rotation = 90)
plot.yticks(rotation = 0)
plot.title('Correlatiojn Map')
plot.savefig('graph.png')
plot.show()

Covariance
np.cov(data.radius_mean,data.area_mean)
print("Cov between radius and area", data.radius_mean.cov(data.area_mean))
print("Cov between radius and fractal",
data.radius_mean.cov(data.fractal_dimension_se))
Cov between radius and area 1224.483409346457
Cov between radius and fractal -0.0003976248576440629
Pearson correlation
p1 = data.loc[:,["area_mean","radius_mean"]].corr(method = "pearson")
print('Pearson correaltion: ', p1)
Pearson correaltion: area_mean radius_mean
area_mean 1.000000 0.987357
radius_mean 0.987357 1.000000
Spearman's Rank correlation
ranked_data = data.rank()
spearman_corr = ranked_data.loc[:,["area_mean","radius_mean"]].corr(method =
"pearson")
print("Spearman's correlation:", spearman_corr)
Spearman's correlation: area_mean radius_mean
area_mean 1.000000 0.999602
radius_mean 0.999602 1.000000
Z-scoring (Normalization)
x = data.area_mean
x_mean = np.mean(x)
x_std = np.std(x)
z = (x-x_mean)/x_std
plot.hist(z,bins=100)
(array([ 1., 3., 2., 7., 9., 10., 16., 13., 13., 19., 28., 28., 30.,
26., 24., 32., 19., 22., 25., 17., 8., 20., 18., 11., 12., 5.,
6., 9., 9., 3., 3., 3., 6., 6., 5., 7., 5., 3., 3.,
6., 6., 3., 7., 4., 4., 6., 5., 6., 4., 6., 2., 2.,
2., 2., 1., 0., 2., 2., 0., 1., 0., 0., 0., 0., 1.,
3., 0., 0., 2., 0., 0., 0., 1., 1., 0., 0., 0., 0.,
0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 2.]),
array([-1.45444309, -1.38739337, -1.32034365, -1.25329393, -1.18624421,
-1.11919449, -1.05214477, -0.98509505, -0.91804533, -0.85099561,
-0.7839459 , -0.71689618, -0.64984646, -0.58279674, -0.51574702,
-0.4486973 , -0.38164758, -0.31459786, -0.24754814, -0.18049842,
-0.1134487 , -0.04639898, 0.02065073, 0.08770045, 0.15475017,
0.22179989, 0.28884961, 0.35589933, 0.42294905, 0.48999877,
0.55704849, 0.62409821, 0.69114793, 0.75819764, 0.82524736,
0.89229708, 0.9593468 , 1.02639652, 1.09344624, 1.16049596,
1.22754568, 1.2945954 , 1.36164512, 1.42869484, 1.49574455,
1.56279427, 1.62984399, 1.69689371, 1.76394343, 1.83099315,
1.89804287, 1.96509259, 2.03214231, 2.09919203, 2.16624175,
2.23329147, 2.30034118, 2.3673909 , 2.43444062, 2.50149034,
2.56854006, 2.63558978, 2.7026395 , 2.76968922, 2.83673894,
2.90378866, 2.97083838, 3.03788809, 3.10493781, 3.17198753,
3.23903725, 3.30608697, 3.37313669, 3.44018641, 3.50723613,
3.57428585, 3.64133557, 3.70838529, 3.775435 , 3.84248472,
3.90953444, 3.97658416, 4.04363388, 4.1106836 , 4.17773332,
4.24478304, 4.31183276, 4.37888248, 4.4459322 , 4.51298191,
4.58003163, 4.64708135, 4.71413107, 4.78118079, 4.84823051,
4.91528023, 4.98232995, 5.04937967, 5.11642939, 5.18347911,
5.25052883]),
<BarContainer object of 100 artists>)