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Prepare the data
Compute the correlation matrix
on Social Networks Create the correlation heatmap with ggplot2
Get the lower and upper triangles of the correlation matrix
Finished correlation matrix heatmap
Reorder the correlation matrix
Add correlation coefficients on the heatmap
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This R tutorial describes how to compute and visualize a correlation matrix using R software and ggplot2 package.

Prepare the data

mtcars data are used :

mydata <- mtcars[, c(1,3,4,5,6,7)]

head(mydata)

## mpg disp hp drat wt qsec

## Mazda RX4 21.0 160 110 3.90 2.620 16.46
## Mazda RX4 Wag 21.0 160 110 3.90 2.875 17.02
## Datsun 710 22.8 108 93 3.85 2.320 18.61
## Hornet 4 Drive 21.4 258 110 3.08 3.215 19.44
## Hornet Sportabout 18.7 360 175 3.15 3.440 17.02
## Valiant 18.1 225 105 2.76 3.460 20.22

Compute the correlation matrix

Correlation matrix can be created using the R function cor() :

cormat <- round(cor(mydata),2)

head(cormat)

## mpg disp hp drat wt qsec

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ggplot2 : Quick correlation matrix heatmap - R software and d... http://www.sthda.com/english/wiki/ggplot2-quick-correlation...

## mpg 1.00 -0.85 -0.78 0.68 -0.87 0.42

## disp -0.85 1.00 0.79 -0.71 0.89 -0.43
## hp -0.78 0.79 1.00 -0.45 0.66 -0.71
## drat 0.68 -0.71 -0.45 1.00 -0.71 0.09
## wt -0.87 0.89 0.66 -0.71 1.00 -0.17
## qsec 0.42 -0.43 -0.71 0.09 -0.17 1.00

Read more about correlation matrix data visualization : correlation data visualization in R

Create the correlation heatmap with ggplot2

The package reshape is required to melt the correlation matrix :

library(reshape2)
melted_cormat <- melt(cormat)
head(melted_cormat)

## Var1 Var2 value

## 1 mpg mpg 1.00
## 2 disp mpg -0.85
## 3 hp mpg -0.78
## 4 drat mpg 0.68
## 5 wt mpg -0.87
## 6 qsec mpg 0.42

The function geom_tile()[ggplot2 package] is used to visualize the correlation matrix :

library(ggplot2)
ggplot(data = melted_cormat, aes(x=Var1, y=Var2, fill=value)) +
geom_tile()

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( Note that, if you have lot of data, it’s preferred to use the function geom_raster() which can be much faster.
Development in R
Specialization: Genomic
Data Science Get the lower and upper triangles of the correlation matrix
Note that, a correlation matrix has redundant information. We’ll use the functions below to set half of it to NA.

See More Resources Helper functions :

# Get lower triangle of the correlation matrix

get_lower_tri<-function(cormat){
cormat[upper.tri(cormat)] <- NA
return(cormat)
analyzing data
}
# Get upper triangle of the correlation matrix
heatmap software
get_upper_tri <- function(cormat){
cormat[lower.tri(cormat)]<- NA
data mapping return(cormat)
}
correlation data

correlation test Usage :

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ggplot2 : Quick correlation matrix heatmap - R software and d... http://www.sthda.com/english/wiki/ggplot2-quick-correlation...

upper_tri <- get_upper_tri(cormat)

R Packages upper_tri

factoextra

survminer ## mpg disp hp drat wt qsec

## mpg 1 -0.85 -0.78 0.68 -0.87 0.42
ggpubr ## disp NA 1.00 0.79 -0.71 0.89 -0.43
## hp NA NA 1.00 -0.45 0.66 -0.71
ggcorrplot ## drat NA NA NA 1.00 -0.71 0.09
## wt NA NA NA NA 1.00 -0.17
fastqcr ## qsec NA NA NA NA NA 1.00

Finished correlation matrix heatmap

Melt the correlation data and drop the rows with NA values :

# Melt the correlation matrix

library(reshape2)
melted_cormat <- melt(upper_tri, na.rm = TRUE)
# Heatmap
Gagnez 30 library(ggplot2)
ggplot(data = melted_cormat, aes(Var2, Var1, fill = value))+
Go de geom_tile(color = "white")+

bonus scale_fill_gradient2(low = "blue", high = "red", mid = "white",

midpoint = 0, limit = c(-1,1), space = "Lab",
internet name="Pearson\nCorrelation") +
theme_minimal()+
Optez pour le theme(axis.text.x = element_text(angle = 45, vjust = 1,

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In the figure above :

negative correlations are in blue color and positive correlations in red. The function scale_fill_gradient2 is used
with the argument limit = c(-1,1) as correlation coefficients range from -1 to 1.
coord_fixed() : this function ensures that one unit on the x-axis is the same length as one unit on the y-axis.

Reorder the correlation matrix

This section describes how to reorder the correlation matrix according to the correlation coefficient. This is useful to iden-
tify the hidden pattern in the matrix. hclust for hierarchical clustering order is used in the example below.
R Graphics Essentials for
Helper function to reorder the correlation matrix :
Great Data Visualization:
200 Practical Examples
You Want to Know for reorder_cormat <- function(cormat){
Data Science # Use correlation between variables as distance
⋆ NEW!! dd <- as.dist((1-cormat)/2)
hc <- hclust(dd)
cormat <-cormat[hc$order, hc$order]
}

Reordered correlation data visualization :

Practical Guide to Cluster # Reorder the correlation matrix

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Analysis in R cormat <- reorder_cormat(cormat)

upper_tri <- get_upper_tri(cormat)
# Melt the correlation matrix
melted_cormat <- melt(upper_tri, na.rm = TRUE)
# Create a ggheatmap
ggheatmap <- ggplot(melted_cormat, aes(Var2, Var1, fill = value))+
geom_tile(color = "white")+
scale_fill_gradient2(low = "blue", high = "red", mid = "white",
midpoint = 0, limit = c(-1,1), space = "Lab",
Practical Guide to
name="Pearson\nCorrelation") +
Principal Component
theme_minimal()+ # minimal theme
Methods in R
theme(axis.text.x = element_text(angle = 45, vjust = 1,
3D Plots in R size = 12, hjust = 1))+
coord_fixed()
# Print the heatmap
print(ggheatmap)

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Go de Add correlation coefficients on the heatmap
bonus 1. Use geom_text() to add the correlation coefficients on the graph
2. Use a blank theme (remove axis labels, panel grids and background, and axis ticks)
internet 3. Use guides() to change the position of the legend title

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Read more about correlation matrix data visualization : correlation data visualization in R

Infos

( This analysis has been performed using R software (ver. 3.2.1) and ggplot2 (ver. 1.0.1)

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