Introduction
Clustering and Heatmap generation using R
Clustering and heatmap helps us to visualize trends in large dataset. Here, this method will describe how to create one in R
Preparing the dataset
Ideal dataset for heatmap is a matrix (preferably as a csv file), where there are rows and columns of data, like this:
$ cat test_dataset.txt
A B C D E F
Row_1 97 14 99 65 57 29
Row_2 56 18 50 8 58 98
Row_3 58 58 43 936 47 78
Row_4 2 55 5 65 48 5
Row_5 45 87 47 47 88 47
Row_6 69 6 69 55 52 88
Row_7 8 32 58 23 23 7
Row_8 6 3 21 32 3 87
Row_9 37 98 36 12 36 7
Row_10 85 75 34 25 2 9
This is a tab separated data, simply use the tr to make it csv file
cat test_dataset.txt | tr '\t' ',' > test_dataset.csv
The new data file should look like this:
$ cat test_dataset.csv
,A,B,C,D,E,F
Row_1,97,14,99,65,57,29
Row_2,56,18,50,8,58,98
Row_3,58,58,43,936,47,78
Row_4,2,55,5,65,48,5
Row_5,45,87,47,47,88,47
Row_6,69,6,69,55,52,88
Row_7,8,32,58,23,23,7
Row_8,6,3,21,32,3,87
Row_9,37,98,36,12,36,7
Row_10,85,75,34,25,2,9
Creating the heatmap
Open R in either Windows/Linux/Mac. You will need following packages for this tutorial. If you don’t have them, please install using the following commands:
install.packages(c("gplots", "vegan", "RColorBrewer", "Cairo"))
install.packages("BiocManager")
BiocManager::install("Heatplus")
Once done, load the necessary libraries to make sure they were installed correctly.
# load required packages
library(gplots)
library(Heatplus)
library(vegan)
library(RColorBrewer)
library(Cairo)
Now we can load the data and generate the heatmap.
# import the data file as matrix
INFILE = "data/test_dataset.csv" # Path to CSV file
all.data <- as.matrix(read.csv (INFILE, sep=",", row.names=1))
all.data[1:3, 1:4] # take a look at your data
#> A B C D
#> Row_1 97 14 99 65
#> Row_2 56 18 50 8
#> Row_3 58 58 43 936
data.prop <- all.data/rowSums(all.data) # convert the data into proportions, you can also log transform your data
data.prop[1:3, 1:3] # view transformed data
#> A B C
#> Row_1 0.26869806 0.03878116 0.2742382
#> Row_2 0.19444444 0.06250000 0.1736111
#> Row_3 0.04754098 0.04754098 0.0352459
# create a color gradient for heatmap
scaleyellowred <- colorRampPalette(c("lightyellow", "red"), space = "rgb")(100)
# generate a heatmap without clustering
heatmap(as.matrix(data.prop), Rowv = NA, Colv = NA, col = scaleyellowred, margins = c(10, 2))
Add clustering.
# Cluster the data, first rows
data.dist <- vegdist(data.prop, method = "bray")
row.clus <- hclust(data.dist, "aver")
# then columns, you can skip one of the clustering if you don't want to mess a particular row/column
data.dist.g <- vegdist(t(data.prop), method = "bray")
col.clus <- hclust(data.dist.g, "aver")
# generate a heatmap
p <- heatmap(as.matrix(data.prop),
Rowv = as.dendrogram(row.clus),
Colv = as.dendrogram(col.clus),
col = scaleyellowred,
margins = c(7, 8),
xlab = "Column names",
ylab = "Row names",
main = "Title", pch=10)
The image is stored as plot p and can be saved as a scalabe vector.
# to save it as scalable vector graphics (change svg to png, pdf etc if you need other formats)
svg("heatmap.svg")
p
#> $rowInd
#> [1] 3 4 8 1 2 6 10 7 5 9
#>
#> $colInd
#> [1] 6 4 2 5 1 3
#>
#> $Rowv
#> NULL
#>
#> $Colv
#> NULL
dev.off()
#> quartz_off_screen
#> 2
You can customize the axis titles, chart title by modifying the commands above.