Corr plot and Pair plots matrix: Python vs R

Correlation heat map in R and Python

Introduction

Correlation is often used to test the relationship between two or more variables. Pearson product moment correlation is the most commonly used method of calculating correlation coefficient. It mainly measures the linear relationship between variables. Spearman and Kendal rank correlations are a non-parametric measures of correlation.

Pearson correlation requires few assumptions to be met: linearity, normality, and absence of outliers. These assumptions should be met before doing the correlation. You can use Shapiro wilk test to to check whether a variable is normally is distributed using a simple command in r: shapiro.test(data$var). This test gives you W statistic and a p value. A p value of greater than 0.05 means you can assume “normally” in your variable.

\[ r_{x y}=\frac{n \sum x_{i} y_{i}-\sum x_{i} \sum y_{i}}{\sqrt{n \sum x_{i}^{2}-\left(\sum x_{i}\right)^{2}} \sqrt{n \sum y_{i}^{2}-\left(\sum y_{i}\right)^{2}}} \] rxy = Pearson r correlation coefficient between ,

n = number of observations

x_i = observed value of x for ith observation, y_i = observed value of y or ith observation

Without spending much time on the theory, let’s go directly to creating a correlation matrix and then we will visualize with a heat map in R and Python. Let’s use the cancer classification data.

For detail explanations. Please check the following video. https://www.youtube.com/watch?v=Z7ggbnj0dM0&t=2s

library(reticulate)
r_data  <- read.csv("cancer_classification.csv")
dim(r_data)

[1] 569  31

colnames(r_data) 

 [1] "mean.radius"             "mean.texture"           
 [3] "mean.perimeter"          "mean.area"              
 [5] "mean.smoothness"         "mean.compactness"       
 [7] "mean.concavity"          "mean.concave.points"    
 [9] "mean.symmetry"           "mean.fractal.dimension" 
[11] "radius.error"            "texture.error"          
[13] "perimeter.error"         "area.error"             
[15] "smoothness.error"        "compactness.error"      
[17] "concavity.error"         "concave.points.error"   
[19] "symmetry.error"          "fractal.dimension.error"
[21] "worst.radius"            "worst.texture"          
[23] "worst.perimeter"         "worst.area"             
[25] "worst.smoothness"        "worst.compactness"      
[27] "worst.concavity"         "worst.concave.points"   
[29] "worst.symmetry"          "worst.fractal.dimension"
[31] "benign_0__mal_1"        

Now, let’s read this in Python. I am using reticulate package to run r and python scripts in one RMD file.

import pandas as pd
py_data  = pd.read_csv("cancer_classification.csv")

The data has 31 variables and 569 observations. I will only select the first six variables for my correlation plot.

Notice in R counting starts from 1 while in Python it starts from 0.

filter_r_data  <- r_data[, c(1:6)]
length(filter_r_data)

[1] 6

dim(filter_r_data)

[1] 569   6

Now in Python:

filter_py_data = py_data.iloc[:,0:6]
len(filter_py_data)
filter_py_data.shape

Next is producing the pearson correlation matrix in R and Python

r_corr_matrix <-  cor(filter_r_data, method="pearson")
r_corr_matrix

                 mean.radius mean.texture mean.perimeter mean.area
mean.radius        1.0000000   0.32378189      0.9978553 0.9873572
mean.texture       0.3237819   1.00000000      0.3295331 0.3210857
mean.perimeter     0.9978553   0.32953306      1.0000000 0.9865068
mean.area          0.9873572   0.32108570      0.9865068 1.0000000
mean.smoothness    0.1705812  -0.02338852      0.2072782 0.1770284
mean.compactness   0.5061236   0.23670222      0.5569362 0.4985017
                 mean.smoothness mean.compactness
mean.radius           0.17058119        0.5061236
mean.texture         -0.02338852        0.2367022
mean.perimeter        0.20727816        0.5569362
mean.area             0.17702838        0.4985017
mean.smoothness       1.00000000        0.6591232
mean.compactness      0.65912322        1.0000000

Now, in Python

py_cor_matrix = filter_py_data.corr(method="pearson")

We have now produced our pearson correlation matrix in both R and Python. Next is visualizing them using corr heat maps. I use correplot package in R and matplotlib and seaborn libraries for producing for producing the correlation heatmaps in both languages

The corrplot() function has numerous additional arguments which you can play with. I will use few of them here.

library(corrplot)
corrplot(r_corr_matrix, method ="shade", addCoef.col=TRUE )

Now, in Python

import matplotlib.pyplot as plt
import seaborn as sns

sns.heatmap(py_cor_matrix, annot=True, cmap="viridis")
plt.show()

I personally like the plot by seaborn. But, it is a personal taste.

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